[gmx-users] Dual Xeon workstation - starting one job/cpu

Hi, Recently I received a dual Xeon ( 2x E5-2630v3) workstation with two Tesla K40c cards. I'm now trying to figure out how to start one job/cpu. For CPU1, this is not a problem: gmx mdrun -v -deffnm test -gpu_id -ntomp 4 -pin on -maxh 0.15 -nsteps -1 #above starts a job on CPU1 with

Re: [gmx-users] color-coding molecule location at different time frame

VMD allows you to color code the trajectory based on the frame number- exactly what you want to do. -g On Wed, Mar 23, 2016 at 5:42 AM, Justin Lemkul wrote: > > > On 3/22/16 12:39 PM, Jagannath Mondal wrote: > >> Dear gromacs-users >>I have a system of protein-ligand

Re: [gmx-users] color-coding molecule location at different time frame

On 3/22/16 12:39 PM, Jagannath Mondal wrote: Dear gromacs-users I have a system of protein-ligand system. I would like to use different color for ligand location at different time-frame. The final goal is to have a snapshot where ligand location of all time frame are color-coded using a

Re: [gmx-users] do_dssp problem

Dear Khatnaa, I would certainly downsample using -dt. Unless, of course, you really need to know the secondary structure over 30 frames. That said, I think do_dssp should be able to handle large trajectories, so this might be a bug in some sense. Kind regards, Erik > On 22 Mar 2016, at

[gmx-users] color-coding molecule location at different time frame

Dear gromacs-users I have a system of protein-ligand system. I would like to use different color for ligand location at different time-frame. The final goal is to have a snapshot where ligand location of all time frame are color-coded using a color-gradient ( for example : red at short time and

[gmx-users] do_dssp problem

Dear Gmx-Users, I had done roughly 300ns peptide and membrane simulation. I am trying to do some analyses through the do_dssp. To get in .xpm file I put .xtc and .tpr files. Then at certain frame its just killed and gave me the empty files with strange names like ddccTf1j, ddmMD9pt,

Re: [gmx-users] Computing dielectric relaxation properties of solutions

Thank you David, I will do it. I have sent a bug report to redmine, but without assigning it. Thanks again, Roberto Il 22/03/2016 15:11, David van der Spoel ha scritto: On 22/03/16 14:37, Roberto Olmi wrote: Dear gmx-users, I apologize for insisting, but it seems strange to me that nobody

Re: [gmx-users] Computing dielectric relaxation properties of solutions

On 22/03/16 14:37, Roberto Olmi wrote: Dear gmx-users, I apologize for insisting, but it seems strange to me that nobody of you has ever been involved in computing the dielectric relaxation properties of a solution (or simply of water). It appears that nobody gets the same error (smallbin

[gmx-users] Computing dielectric relaxation properties of solutions

Dear gmx-users, I apologize for insisting, but it seems strange to me that nobody of you has ever been involved in computing the dielectric relaxation properties of a solution (or simply of water). It appears that nobody gets the same error (smallbin double linked list corrupted) I obtain

Re: [gmx-users] Tesla K40 vs GeForce GTX TITAN X

On 3/22/16 6:41 AM, Nikhil Maroli wrote: Dear all, Which GPU is better for GROMACS simulation Tesla K40 or GeForce GTX TITAN X ,we have enough fund to buy K40 but by comparing price i could get two or three GeForce GTX TITAN X for one Tesla K40 , which should be better for MD studies

Re: [gmx-users] Rmsd Problem

There is no attachment i can see. BTW from literature and knowledge in your typical problem will help to analyse results. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Tesla K40 vs GeForce GTX TITAN X

Dear all, Which GPU is better for GROMACS simulation Tesla K40 or GeForce GTX TITAN X ,we have enough fund to buy K40 but by comparing price i could get two or three GeForce GTX TITAN X for one Tesla K40 , which should be better for MD studies especially in GROMACS ? if i use two or three GPU in

[gmx-users] Rmsd Problem

Deaer Gromacs users, I have a problem in analyzing my MD simulation results of RMSD the graph of apo protein lies below while the graph lines of ligand bound complexes lies above.I am not getting what this graph is showing. Kindly give me some clues to interpret this graph. Here I am attaching

Re: [gmx-users] Error: not enough memory

Allright I installed from source. Will do it again. Thank you very much NIkhil, once again. On Tue, Mar 22, 2016 at 11:35 AM, Nikhil Maroli wrote: > Hi, > this is problem regarding g_mmpbsa > > your not provided required information such as Gromacs version and > g_mmpbsa >

Re: [gmx-users] GPU configuration suggestions

Hi Nikhil, please take a look at http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full A great deal of your questions are answered there! Best, Carsten > On 22 Mar 2016, at 06:52, Nikhil Maroli wrote: > > Dear all, > > we would like to purchase one GPU enabled

Re: [gmx-users] Error: not enough memory

Hi, this is problem regarding g_mmpbsa your not provided required information such as Gromacs version and g_mmpbsa installation from source or binary ?! in common if you using Gromacs 5.1.1 install g_mmpbsa from binary package instead of compiling from source -- Gromacs Users mailing list *