[gmx-users] how to differentiate crystal water and explicit waters in gromacs ???

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 23 08:47:15 CET 2011

On 23/03/2011 4:42 PM, Praveen Kumar Madala wrote:
> Hi,
> I am new to GROMACS and I am trying to perform a MD run in PBC 
> condition with water as solvent.
> I want to keep the crystal water molecules different from explicit 
> waters,  I believe this helps me in analysis of crystal waters.

You can set up an index group to label them, and then use a 
visualization or other analysis program to see what they do. This 
doesn't require doing anything prior to the simulation. See manual and 
webpage for resources describing use and construction of groups.


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