7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. From: Gianluca Interlandi (gianluca_at_u. uiuc. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. Kisiela and Hovhannes Avagyan and Della J. I needed to install the 'patch' program. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. washington. Gianluca has 2 jobs listed on their profile. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Previous message: Gianluca Interlandi: "NAMD 2. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). washington. Facebook gives people. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. Deadline is this Friday (or in three > months). I would be > happy if somebody could point me out to some scripts which help me performRe: checkpoint software for NAMD? From: Gianluca Interlandi (gianluca_at_u. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. PMID: 37700555; DOI: 10. 6 version, although I am not running the cluster at full load yet. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). how to output more significant figures in a file for energies and forces? Next message: Gianluca Interlandi: "Re: accuracy of measurement"Reply: Gianluca Interlandi: "Re: Force field design" Messages sorted by: [ attachment ] On 07/24/2014 12:03 AM, R. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. I needed to install the 'patch' program. , Thomas W. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. I was recording the energies once every 100 steps. Semantic Scholar's Logo. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. > > According to your banchmarks, it looks like the less expensive GTX285. C; the more troublesome part is the lack of long-range electrostatic treatments. Balcony. washington. Fwd: Installing NAMD on windows. washington. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. 7 with the PLUMED patch. Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. From: Gianluca Interlandi (gianluca_at_u. 100% refund of amount payable if you cancel at least 14 days before check-in. washington. washington. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Entertainment. C; the more troublesome part is the lack of long-range electrostatic treatments. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. 15 K 1 KT = 2. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. Comparative controls consisted of FocH (high affinity with and. From: Gianluca Interlandi (gianluca_at_u. 6 version, although I am not running the cluster at full load yet. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Re: namd ibverbs. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Languages: English, Spanish, Italian. The read speed of the trajectory will go much faster if you select the "load all at once" checkbox in the moleculeRe: Vibrational mode analysis. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. MyOne Bedroom Apartment, Sleeps 3 - C$150 avg/night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum 2 night(s) stay Bookable directly online - Book vacation rental 11131246 with Vrbo. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. edu > <mailto:gianluca_at_u. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. uiuc. 7 out the door on Friday. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. edu> wrote:Gianluca Interlandi. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. uiuc. From: Gianluca Interlandi (gianluca_at_u. What this rental offers. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. edu) Date: Tue Oct 17 2006 - 00:36:56 CDT Next message: Jacob Poehlsgaard: "Intel Woodcrest version?" Previous message: Jim Phillips: "Free Linux Cluster-Building Workshop - 30 Nov 2006 - 01 Dec 2006" In reply to: Gianluca Interlandi: "SMD and restart"> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Sarah Keller Professor. Policies. > > Forget about creating a pdb file. washington. VMD-L Mailing List. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. prm". washington. washington. The more tasks you have the > more frequently the CPUs need to update each other. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. com) Date: Fri Aug 30 2013 - 18:19:04 CDT Next message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" Previous message: Gianluca Interlandi: "Re: editing the code of the non bonded pair potentials" In reply to:. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. Biochemistry. 1 the measure command of VMD can also > calculate the energy: > > energy energy_term atom_list [parameters] [options]: Returns the > specified energy term for a given set of atoms. edu]Reply All Saturday,. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). running multicore version on a 2-CPU node. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. Re: Protein in/out of box. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. washington. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Member since 2014. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. 7 out the door on Friday. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. I would be > happy if somebody could point me out to some scripts which help me performDCD. From: Gianluca Interlandi (gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. Eric Klavins Professor. washington. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. eduRe: Question about equilibration. Re: Vibrational mode analysis. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. mx: "Re: Fat node" Previous message: Dan Strahs: "checkpoint software for NAMD?" In reply to: Dan Strahs: "checkpoint software for NAMD?". washington. washington. washington. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. Biochemistry. washington. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated lectin domain (LD) that binds mannose on the. washington. Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce the. washington. 1 2 3 Barry Lutz starts tenure-track position, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professor UW Bioengineering is pleased to announce. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. washington. washington. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. 7b1 on NCSA. Hi I’m Yiming Li, and I’m a senior in bioengineering. Facilities. Re: replica exchange and GPU acceleration. edu) Date: Tue Sep 15 2020 - 20:34:44 CDT Next message: Kodituwakku,Dimuthu Nirmani: "Re: Post processing NAMD trajectory" Previous message: Victor Zhao: "Re: Re: AMBER input and REST2 leads to crash" Next in thread:. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. washington. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. I > > attach a plot of a constant velocity simulation where I'm pulling twoRe: NAMD 2. 97 pN*nm = 1 Kcal/mol In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. washington. Kid friendly. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. uiuc. Just source the Tcl file and use the 'unwrap' procedure. Here they are: a. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. In the NAMD folder that you downloaded there >> is a file called "notes. I know this can be just a detail, but it is quite tricky. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. washington. washington. edu> > wrote:From: Gianluca Interlandi [gianluca_at_u. I would like to erase Windows and install Leap 42. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Re: NAMD 2. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. PMID: 37700555; DOI: 10. Write a review. washington. Rachel Klevit WRF Endowed Chair in Biochemistry. Living Room. Jennifer KongRE: DCD. I'm testing specifically this protein for its beaviour. Stenkamp, 3 Wendy E. Michel Espinoza-Fonseca: "Re: Vibrational. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. 26588. Specifically, I’m testing different binding domains. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. You can specify the nice priority in a nodelist file, for example: group main ++nice 19 host machine1 ++nice 20 host machine2 ++nice 21 host machine3> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Previous message: Gianluca Interlandi: "NAMD 2. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. On Thu, Oct 20, 2011 at 05:48:32PM -0700, Gianluca Interlandi wrote: > Dear VMD users, > > A while ago I bothered this list asking for recommendations for a > lightweight laptop to buy which would support a decent 3D acceleration in > order to use VMD in presentations. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Michel Espinoza-Fonseca: "Re: Vibrational. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. Bathrooms: 1. Forest, Academic Editor. washington. What can be the possible cause for this or does it happens naturally> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. Search for: Main Menu. This is unrelated to KDE3. From: Gianluca Interlandi (gianluca_at_u. Join Facebook to connect with Gianluca Interlandi and others you may know. There have been over 180 downloads and no complaints so far. washington. washington. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. edu) Date: Sat Jul 04 2015 - 15:33:25 CDT Next message: VINAYAK BHAT: "Generating solvent models. Sarah Keller Professor. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). From: Gianluca Interlandi (gianluca_at_u. From: Axel Kohlmeyer (akohlmey_at_gmail. edu>> > > I suspect that E3_19 might not be stable with this type of > implicit solvent model (it doesn't contain a term to take the > non-polar solvation energy into accout). Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. I would be > happy if somebody could point me out to some scripts which help me performRe: Help building a desktop for namd. From: Gianluca Interlandi (gianluca_at_u. washington. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. e. washington. Justin Kollman Professor. washington. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallRe: Help building a desktop for namd. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. washington. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. uiuc. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. I empolyed PBC condition with wraping water and wraping all options on. edu> > wrote: > are other people also using those GPUs? > >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. edu on behalf of Gianluca Interlandi [gianluca_at_u. Whitfield, 2 Esther Bullitt, 4 Ronald E. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. From: Gianluca Interlandi (gianluca_at_u. washington. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. J. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Re: Abe versus Lincoln. INVENTING THE FUTURE OF MEDICINE. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. 7 released. Rooms and beds. Sokurenko 1 , *. washington. Check the NAMD log! Any errors or warnings?"wrapAll on" with a complex. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. washington. Both > simulations were started from X-ray structures. washington. Re: query about wrapped coordinates. washington. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Neil King Assistant Professor. 0 and 2. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Choose File -> Save Coordinates. 6 ns/day for a 100k atom system with roughly those same parameters (and. Biochemistry. Gianluca Interlandi. edu> wrote: > Hi Fatemeh, >> On Wed, Dec 12, 2012 at 12:26 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. I wonder whether anybody > has had the same problem and found a solution. washington. It is experimentally knownReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. Michel Espinoza-Fonseca: "Re: Vibrational. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. washington. washington. Cancellation policy. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. washington. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. washington. This school has it's > own biophysics division. VMD-L Mailing List. washington. First of all, I am sorry to bother you again for problem. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. washington. From: Gianluca Interlandi (gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. Choose File -> Save Coordinates. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. washington. , "not (water or ions)" GianlucaRe: DCD. , and Thomas W. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"UW Bioengineering is pleased to announce the hires of faculty Barry Lutz and Gianluca Interlandi, as well as the promotion of Suzie Pun to full professor. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. washington. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. On the other hand, a 4 TB WD 7200RPM is under 200$. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. You should simulate it in explicit water (or try one of the implicitIn reply to: Gianluca Interlandi: "What, if no temperatue control specified?" Messages sorted by: [ attachment ] Hi! A technical question. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. washington. From: Gianluca Interlandi (gianluca_at_u. I made those videos seven years ago. Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthRe: NAMD 2. Research Assistant Professor [email protected]> > wrote:VMD-L Mailing List. m. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. 26588 Item in Clipboard Cite. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. Thanks for the reply. Bathroom 1. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. I wanted to briefly update here on my > experience. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. washington. washington. MyFrom: Gianluca Interlandi (gianluca_at_u. From: Axel Kohlmeyer (akohlmey_at_gmail. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. Search for: Main Menu Author Summary A common approach in the development of selective inhibitors for ligand-receptor interactions is targeting the receptor binding site with the expectation that inhibitors will sterically interfere with ligand binding and thus block receptor function via a competitive (orthosteric) mechanism. edu] Sent: Monday, June 20, 2016 12:46 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. In the text field you can enter your atom selection, e. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. washington. edu> > wrote: > are other people also using those GPUs? > > From: Gianluca Interlandi (gianluca_at_u. Previous studies. From: Gianluca Interlandi (gianluca_at_u. Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u.