[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
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users