[gmx-users] PBC after energy minimization

Justin Lemkul jalemkul at vt.edu
Sat May 2 13:48:51 CEST 2020

On 5/1/20 9:29 AM, John Whittaker wrote:
> Hi Mohamed,
>> Hello everybody,
>> In order to solve the PBC at the end I use the command:
>> *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol *
>> followed by:
>> *gmx trjconv -s md_0_1.tpr  -f md_noPBC.xtc -o md_noPBC.pdb*
>> I want to solve this problem after the energy minimization but I don't
>> have
>> .xtc file to use it as I do at the end.
>> How can I solve this problem after the energy minimization ?
> You're saying that your energy minimization does not produce a trajectory
> (a .trr or .xtc file)?
> If that's the case, you just have to instruct GROMACS to periodically
> write to a trajectory file using options in the .mdp file (namely,
> nstxout). Take a look at:
> http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
> Under the section "output control" you will find what you are looking for.

"Trajectories" from energy minimization are generally unreadable as the 
interval of saved frames is uneven. During EM, a frame is only written 
when the energy goes down, which is not necessarily every possible 
frame. I also seem to recall that there is never XTC output from EM, 
even if requested, because it's rather pointless. Maybe that has changed.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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