[gmx-users] Is GPU GTX 560 compatible with GROMACS?

Dear All, Can you please guide me on how to find out if GeForce GTX 560 GPU card by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti is mentioned, but GTX 560 is not. Thanks, G -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of

Re: [gmx-users] Is GPU GTX 560 compatible with GROMACS?

Dear Shouliang, Thanks. Maybe the developers can help undertand why GTX560 is not included on the GPU compatibility list for GROMACS? -G 2012/4/16 shouliang dong : > It is compatible with GROMACS. > > 在 2012年4月14日 上午11:32，Gaurav Goel 写道： >> >> Dear All, >> >>

Re: [gmx-users] MD simulation with varying pH

t > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Gau

Re: [gmx-users] TRACE OF RMSD COMPARISON MATRIX

Following link might be helpful: http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html -g -- Gaurav Goel Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India On 02-Jul-2013, at 10:45 AM, Richa Singh

Re: [gmx-users] position restraint

e list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Del

[gmx-users] Nonequilibrium MD- implementing a temperature gradient simulation

My aim is to establish a temperature gradient in the MD simulation box. I'm simulating a magnesium silicate system with interatomic potentials (Mg-Mg, Mg-Si, etc.) and no bond or angle potentials. My algorithm: 1. Divide the MD box in 12 slabs along the x-axis. 2. Pick slab 3 as my source and sla

[gmx-users] reading velocity in the g_msd routine

Hello gmx-users users :) I am modifying the 'g_msd' utility to be able to calculate viscosities using the corresponding Einstein relationship according to equation 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is similar to the mean-square displacement equation for self-diffusion

Re: [gmx-users] enegry minimisation

After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion

Re: [gmx-users] enegry minimisation

On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul wrote: > > > Gaurav Goel wrote: >> >> After adding water you can do energy minimization (EM) in two steps: >> >> 1. Constrain the protein backbone and do EM. >> 2. Now do EM on the full system. >> 3.

Re: [gmx-users] enegry minimisation

;     8     1  1000  1000  1000 >>     9     1  1000  1000  1000 >>    11     1  1000  1000  1000 >>    12     1  1000  1000  1000 >>    15     1  1000  1000  1000 >>    18     1  1000  1000  1000 >>    19     1  1000  1000  1000 >>    20     1

[gmx-users] how small rcoulomb can be

For my NPT/NVT simulations I'm using a BKS potential for dispersion interactions (VdWtype=USER) which has a cut-off of 0.55 nm. I also set rcoulomb=rlist=0.55 nm. My first question is regarding the choice of rcoulomb=0.55nm. Any thoughts on whether this rcoulomb is large enough to ascertain that

Re: [gmx-users] how small rcoulomb can be

Thanks for your reply Mark. On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham wrote: > > > - Original Message - > From: Gaurav Goel > Date: Thursday, June 17, 2010 5:21 > Subject: [gmx-users] how small rcoulomb can be > To: Discussion list for GROMACS users > >&

Re: [gmx-users] how small rcoulomb can be

I will re-ask my question as it didn't come out right in previous mail. Read below. On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham wrote: > > > - Original Message - > From: Gaurav Goel > Date: Thursday, June 17, 2010 5:21 > Subject: [gmx-users] how small rcoulomb

[gmx-users] problem install gromacs in parallel

I'm trying to install a local copy of GROMACS on Ohio Super Computer. I was able to build single and double precision versions (did make distclean after each), however, got errors while installing parallel version. I will appreciate you taking time to help with this installation. Thanks. This is

Re: [gmx-users] vdwtype=shift

section 7.3.11 of gromacs manual (v4.0)/ -Gaurav On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund wrote: > you zou skrev: >> >> Dear users, >> >> I have a question about vdwtype. My question is if I use vdwtype=shift in >> nvt.mdp file: >> >> ; Neighborsearching >> ns_type = grid ; search neighbor

[gmx-users] Should I use separate PME nodes

I ran my simulation in parallel on 4 nodes (with zero separate PME nodes). Below is the information printed in md.log. I see that PME-Mesh calculations took 60% of CPU time. Any recommendations on using 1 or more separate PME nodes to speed up? Computing: M-Number

Re: [gmx-users] Problem with Lennard Jones cross terms

By specifying both c6 and c12 to be zero, you've set both the attractive and repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to zero. If you don't have any electrostatic repulsions in your system polymer might be "attracted" to Silica substrate for entropic reasons...e.g., cen

Re: [gmx-users] Problem with Lennard Jones cross terms

le? > You can switch-off all non-bonded interactions between a pair of energy groups by defining Energy group exclusions. Sec. 7.3.19 of the gromacs manual 4.0. -Gaurav > > Thanks again, Chrysostomos > --- Στις *Πέμ., 01/07/10, ο/η Gaurav Goel *έγραψε: > > > Από: Gaurav Goel &g

Re: [gmx-users] g_msd

On Mon, Jul 12, 2010 at 5:22 PM, Ricardo Cuya Guizado wrote: > Dear gromacs users > I make a MD of 20 ns of a solute in water > With the g_msd program the msd vs the time was obtained > In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a > plateau with no linear tendence at

Re: [gmx-users] extracting coordinates

What do you want to do with the coordinates? Look-up 'trjconv' -Gaurav On Tue, Jul 20, 2010 at 11:32 AM, Vishal Agarwal wrote: > Dear All, > I am new to using GROMACS. I have done some NVT simulation on glucose > molecule. Can one anyone tell me how to extract the coordinates of atoms for > eac

[gmx-users] does generating velocity keep centre of mass motion zero?

I'm doing NVE simulations so I've set comm_mode=None. Now my questions is regarding the generation of initial velocity with this- gen_vel = yes gen_temp= 4000 ; initial temperature gen_seed= 10234 The reason I do not want to use velocities

Re: [gmx-users] Reduced Units

On Mon, Aug 9, 2010 at 9:58 AM, wrote: > Hi, > > I want to use the pme algorithm in GROMACS. Thge size of my box is > 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 > of CO2 molecules. If I am using reduced units, the values of the > parameters "rcoulomb=0.9" I think should b

Re: [gmx-users] RE: log files

You've set the frequency of writing to log file as 'nstlog = 10'. Given that 'nsteps = 1', you're writing to the log file only 1000 times. Do you get a 20GB md.log file with these settings? -Gaurav On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain < nimeshjain2...@u.nort

Re: [gmx-users] RE: log files

w days. > > Did you re-compile using grompp after changing nstlog? Otherwise in md.tpr (output of grompp), nstlog=1000. -Gaurav > > On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel wrote: > >> You've set the frequency of writing to log file as >> 'nstlo

Re: [gmx-users] Speeding up simulation

Sapna, Is there a particular reason you're using a box so much larger than the droplet diameter? If your only concern is that periodic images should not see each-other maybe you can use a box length=droplet diameter+2*largest cut-off in the system. Also using a more spherical box shape such as r

Re: [gmx-users] Speeding up simulation

Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters* Volume 406, Issues 1-3