[gmx-users] about the traj modification

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 14 18:18:05 CET 2010

zh.li wrote:
> Dear Justin,
>      Thanks for your instant reply about my problem. I've already
> finished the make_ndx part, choosing the "protein" option. But for
> trjconv, how can I write the command line to have the prompt "Select
> group for output"? Sorry, I'm really a beginner. Thank you!

If you only want to write out protein coordinates, there is no need to make any 
special index groups.  "Protein" is one of the default groups read from the 
input by all Gromacs tools.  Run trjconv on your trajectory and you will be 
prompted to "Select group for output."


> Best,
> Zhenwei
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: 2010年1月13日 0:21
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] about the traj modification
> 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."
> -Justin
>> 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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