[gmx-users] Virtual Sites - remove from GRO

Justin A. Lemkul jalemkul at vt.edu
Mon May 14 14:50:03 CEST 2012

On 5/14/12 8:42 AM, Steven Neumann wrote:
> Dear Gmx Users,
> i run the implicit simulation with virtual sites on the hydrogen of my protein.
> Now I want to extract coordinates and run another simulation (in explicit
> solvent). Is there any way to remove those virtual sites from my gro file as VMD
> write the file using atoms not recognized by pdb2gmx obviously? Please, help!

Virtual sites have rather obvious names that lend themselves well to being 
grepped out, i.e.:

grep -v "M[CN]" conf.gro > conf_clean.gro

Adjust the number of atoms in conf_clean.gro and proceed.



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


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