[gmx-users] spatial restraints

Simon Kit Sang Chu simoncks1994 at gmail.com
Tue Jun 19 04:12:10 CEST 2018

Hi Stefano,

You may consider "gmx make_ndx" to make an index file and append a
restraint section (POSRES) at the end of your existing topology to call the

I think this is a minimal alteration to your topology.


在 2018年6月19日週二 08:17,Stefano Guglielmo <stefano.guglielmo at unito.it> 寫道:

> Hello gromacs users,
> I would like to know if it is possible to add spatial restraints to a
> selected subgroup of atoms of my system (protein+membrane+ligand+water)
> without generating a new topology: I have a top generated with parmed fed
> with the suitable amber ff and I would like just to add the atoms that
> should be restrained to the existing topology.
> Thanks in advance
> Stefano
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