[gmx-users] Re: Problem running free energy simulations

Michael Shirts mrshirts at gmail.com
Thu Oct 3 12:56:36 CEST 2013

Hmm. This really isn't quite enough information to go on.  Can you
file a redmine issue, and include the files used to generate the run
that crashed (.mdp, .gro,. .top), as well as the files that show it
failing (.log)?


On Thu, Oct 3, 2013 at 4:32 AM, Jernej Zidar <jernej.zidar at gmail.com> wrote:
> Dear Michael.
>   The simulations at each lambda point starts from the same structure
> that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has
> ~7500 atoms in a box the size 5 nm x 5 nm x 5 nm.  The molecule of
> interest is located in the center of the unit cell.
> Thanks,
> JErnej
>> Sounds like the simulation is blowing up.  How soon does it start crashing.
>> Also, what configurations are you using to start your free energy
>> simulations at each lambda?
> --
> Windows: Re-Boot, Linux: Be-Root.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at 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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list