[gmx-users] about the traj modification

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 13 00:20:30 CET 2010

zh.li wrote:
> Dear all,
>      I want to remove the water molecules in the original traj file 
> (run.xtc) to save the space, so that I should use the command “trjconv”. 
> But I don’t know which sub-command I should use to realize that? Does 
> anyone here know how to do it? Thank you very much.

You'll need an index group that defines all non-solvent atoms (easily done with 
make_ndx).  Pass the index file to trjconv and simply choose your non-solvent 
group when prompted "Select group for output."


> Zhenwei Li


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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