Re: [gmx-users] GROMACS mdrun

Hi, What are all the GROMACS commands you have been using for this simulation? Why do you think it is not finishing all the steps? Mark On Sat, 15 Oct 2016 10:55 Shilpa Janarthanan wrote: > Hi, > While running an MD job for 10 ns, the system restarts in the final step of > MD (mdrun -v -deffnm

[gmx-users] GROMACS mdrun

Hi, While running an MD job for 10 ns, the system restarts in the final step of MD (mdrun -v -deffnm md) This happens continuously, and the data are not generated. What system settings should I make, to make it run continuously until finishing all the steps? Thank you. -- Shilpa J Department of

Re: [gmx-users] gromacs mdrun problem

Hi, The list does not accept attachments, unfortunately. However, your problem is probably solvable via the advice at http://www.gromacs.org/Documentation/Terminology/Blowing_Up. There's also probably no reason to do a run with position restraints for urea in water, since there's little that is sp

[gmx-users] gromacs mdrun problem

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am attaching my em.mdp and pr.mdp file below- Thanks in advance -- Gromacs Users mailing list * Please search the archive at http:/

Re: [gmx-users] Gromacs mdrun for k20 and cpu

Don't use the GT 610, it's just going to make the run slower. -- Szilárd On Tue, Nov 3, 2015 at 10:37 AM, Alex Mathew wrote: > Hi to all, > > im new to gromacs, Im performing Tutorials my system has 2 x Intel® > E5-2650V2 Processor (8Core) +2 GPU (Tesla k20 and Gt 610) installed gromacs > GPU v

[gmx-users] Gromacs mdrun for k20 and cpu

Hi to all, im new to gromacs, Im performing Tutorials my system has 2 x Intel® E5-2650V2 Processor (8Core) +2 GPU (Tesla k20 and Gt 610) installed gromacs GPU version and total 16 core and 32 threads available in proc. please share me the command to use both gpu and processor for MD (mdrun comman