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
.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:


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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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