[gmx-users] Virtual Sites - remove from GRO

Steven Neumann s.neumann08 at gmail.com
Mon May 14 15:13:05 CEST 2012

On Mon, May 14, 2012 at 1:51 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 14/05/2012 10:42 PM, 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!
> If your original pdb2gmx workflow with virtual sites was recorded in a
> shell script you'd
> a) have a record for when you go to write up, and
> b) be able to do this change easily.
> As it is, a few minutes with a text editor would probably work for small
> systems. Alternatively
> grep -v MCH3 in.gro > temp.gro
> will remove all of the lines for virtual sites named MCH3. Do that for
> each type of virtual site. Adjust the count of atoms at the top of the .gro
> file suitably at the end.
> Mark

Thank you Mark!


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