[gmx-developers] Re: NMR refinement

santhosh mesanthu at gmail.com
Sat Jan 26 04:57:37 CET 2013

Hello All, a final confirmation on a few things:

I did all the things required :
1). Extracted the last frame from trr file. 
2). Wrote a code which calls custom function to compute forces based on
present co-ordinates. (In this case, parallel simulations)
3). Returned the force and added to the existing force from FF. 

While extracting the last frame from trr file, I observed that as the
simulation proceeds, trjconv starts increasing time required to
extract(though not too significant) but to counter that, I took inspiration
from write_traj to write out a XYZ file. (Was able to write one).

I just want a confirmation if not anything : if my .mdp file had options to
remove center of mass motion(of only the protein), is there a possibility
that I would have atom jumps between periodic boxes in the XYZ file written
directly during the simulation. 

Thanks a lot for your patience and replies. 

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