On 11/19/13 11:13 AM, Asaminew Haile wrote:
Hi Gromacs Users
I'm new for gromacs analysis

I'm running MD in a 40 ns time interval. I want to strip the water and
re-image the molecule. But I found that only if I trjcat all trajectories
from the start I can be able to re-image them.
Can someone show me how to re-image them independently?
Here is what I want

for every x in 1000
echo 1  | trjconv -s md.($x+40).tpr -f md.($x+40).xtc -o strip.($x+40).xtc
  -pbc nojump # strip water and re-image

The use of -pbc nojump assumes that the reference frame is suitable for removing jumps. If you have individual .tpr files that correspond to the different trajectories, they may have different reference positions and you won't necessarily get what you want.

The easiest method is (assuming each trajectory is topologically identical and differs only in its coordinates) to create a single reference .tpr file that is suitable for removing jumps.

Most of that information and other useful trjconv help can be found at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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