[gmx-users] Basic questions.

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 26 17:31:52 CET 2008

Quoting fabracht sdf <fabracht at gmail.com>:

> Hello. This is my first time writing an e-mail to this list. So, please
> apologize if I am doing anything wrong.
> I have a basic question about gromacs. How do I restrain certain atoms in my
> protein. I've tried to create an ndx file with the residues i would like to
> restrain and then I created an itp file using posre. But how do I include
> these restrain forces to my topology file? This path I've made, is this
> correct?
> Thank you

You mean, you used genpr to create a new posre.itp file?  That would be the way
to go.  Then just include the new posre.itp file as you would any other. 
Assuming you have a topol.top from pdb2gmx, look at how other topologies are
included.  That should tell you how to use your new .itp file.  Have a thorough
look through Chapter 5 of the manual for information about topologies if this is
still unclear.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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