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

[Justin Lemkul]

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

-- 
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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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