Re: [gmx-users] GROMACS mdrun

[Mark Abraham]

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 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 Bioinformatics,
> SASTRA University.
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Re: [gmx-users] gromacs mdrun problem

[Mark Abraham]

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 special about your starting configuration. See
also http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents.

Mark

On Mon, Oct 3, 2016 at 8:25 AM ISHRAT JAHAN  wrote:

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

[Szilárd Páll]

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 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
> command),
>
>  Thank you very much.
>
>
> Yours sincerely
>
> Alex
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