[gmx-users] Gromacs-4.6 on two Titans GPUs

Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7 cpu with dual GeForces Titans gpu mounted. With this config I'd like to perform simulations using cpu as well as both gpus simultaneously. What flags besides cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_

Aw: [gmx-users] DPOSRES and energy minimization

all-bonds and none work, so I assume, as alternating between these settings speeds up the EM.  However, I always see the protein move around in the box after centering, so just re-center after reaching pressure and temp stability before the extended pre-run equilibration with set restraints (which

[gmx-users] Re: trjconv for pbc

That last procedure works. I really appreciate your help. The only other question I have is related to the selection process. Is there a way to select the oxygen atoms of water within a certain distance of a molecule, as well as the corresponding hydrogen atoms on the water molecule? Right now,

Re: [gmx-users] energy minimization problem

On 11/3/13 6:20 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtolshould be lower than 1. As I understa

Re: [gmx-users] DPOSRES and energy minimization

On 11/3/13 12:38 AM, Gianluca Interlandi wrote: Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: Depending on the forces present in the system, it is possible that the a

Re: [gmx-users] Re: trjconv for pbc

On 11/3/13 7:12 AM, rankinb wrote: That last procedure works. I really appreciate your help. The only other question I have is related to the selection process. Is there a way to select the oxygen atoms of water within a certain distance of a molecule, as well as the corresponding hydrogen a

[gmx-users] Help to simulate gas mixture

Dear Friends, I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas mixture, the same as mixture of O2 and N2, any help(the same as introducing a reference, not GROMACS manual b/c there is no explanation about gas mixture) is appreciated. Kind Regards, Ali -- View this message in

Re: [gmx-users] Help to simulate gas mixture

The principle is the same as at http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents On Nov 3, 2013 6:55 PM, "ali.nazari" wrote: > Dear Friends, > > I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas > mixture, the same as mixture of O2 and N2, any help(the same as intro

Re: [gmx-users] DPOSRES and energy minimization

Is there a way to tell from the log file whether positional restraints are really activated or not? Thanks, Gianluca On Sun, 3 Nov 2013, Justin Lemkul wrote: On 11/3/13 12:38 AM, Gianluca Interlandi wrote: Is it possible to use position restraints: define = -DPOSRES during an energ

[gmx-users] g_lie useage

dear gmx users i am trying to use g_lie tool regarding the fact i am a newbie to this. so i searched through the web for an appropriate protocol. although there are lots of staffs discussing the theory, but i couldn't find any thing describing the steps techniqally and with some details. genera