On 1/14/13 3:02 PM, santhosh wrote:
Hello
For some reasons, I want to output pdb file output after every step of the
MD run. After searching the forum, I found that Gromacs does that only in
some circumstances(like when the system is about to crash or already
crashed).
http://gromacs.5086.n6.nabble.com/turn-off-pdb-output-td4417229.html#a4417301
Is there a way I could have a control on that by changing a flag and can I
write only the protein part ignoring the solvent?
Why not just set nstxtcout = 1 with xtc-grps = Protein? trjconv -sep will then
write separate coordinate files in whatever format you choose after the run.
Anything else would require modification of the code.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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