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

[Michael Shirts]

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)?

http://redmine.gromacs.org/

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?
>
>
>
>
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