[gmx-users] Turn on pdb output after every step

Justin Lemkul jalemkul at vt.edu
Mon Jan 14 21:05:53 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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