[gmx-users] g_saltbr speed

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 12 14:17:01 CEST 2012

On 7/12/12 8:15 AM, Kavyashree M wrote:
> Dear Sir,
> I had a problem again during g_saltbr calculation it needs
> .xtc and .tpr file, I can reduce the .xtc file to have only
> protein but .tpr file will have water also in it. inorder to generate
> new tpr file without water using grompp, i need topology file
> without water .. so do you suggest me to go this way.. it
> appears quite complicated!

In fact, it's quite easy with tpbconv.  From tpbconv -h:

"3. by creating a .tpx file for a subset of your original tpx file, which is
useful when you want to remove the solvent from your .tpx file, or when you
want to make e.g. a pure Calpha .tpx file. Note that you may need to use
-nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not
fully functional."



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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