[gmx-users] I can't re-image molecule for multiple MD without trjcat them from start

[Justin Lemkul]

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
> do
> 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
> done
>

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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