Dimitar Pachov wrote:
Hello,
I have performed simulations of protein+ligands (solute) in truncated
octahedral unit cell of waters (solvent). I would like to retain the
shape of unit cell and have the solute centered in such a way as to be
completely surrounded by solvent. At this point, I cannot achieve this
although I have exhausted my knowledge about using the trjconv options.
My question is:
1. How can one recenter solvent around solute and at the same time keep
the original unit shape?
I used the following command to get this picture:
trjconv -f run.xtc -s run.tpr -n index-all.ndx -o traj/run-test.xtc -pbc
mol -center -ur compact
Use -ur tric instead of -ur compact.
-Justin
where for centering the solute was used and the whole system was saved
to the output trajectory.
Thanks,
Dimitar
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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