[gmx-users] Virtual Sites - remove from GRO

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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