[gmx-users] Virtual Sites - remove from GRO

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 14 14:51:39 CEST 2012

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.


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