Ok, so here's the thing:
my research group have developed a software to track water molecules during
MD simulations. Right now we are working on a feature that will allow us to
track different kind of molecules during one analysis. So I thought it will
be great to test it using different names for 'different kinds' of water
molecules - for example CRY for waters from the crystallographic model and
WAT for others.
So, yes, I could note the residue number, but it will be easier for me to
have CRY and WAT water molecules to track them with our soft. Can I make
pmemd run this kind of simulation?
Best regards,
Karolina
2017-04-05 13:55 GMT+02:00 David A Case <david.case.rutgers.edu>:
> On Wed, Apr 05, 2017, Karolina Mitusińska (Markowska) wrote:
> >
> > thanks for your response.
> > I would like to have two (or more) residues, named for example CRY for
> > crystal water and WAT for water from the water box, both treated by pmemd
> > like water residues.
>
> Just to restate what Hannes said, in different words: just note down the
> residue numbers that correspond to the "crystal" waters, and use residue
> numbers rather than names to follow their behavior during a simulation.
>
> ....good luck...dac
>
>
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Received on Wed Apr 05 2017 - 05:30:03 PDT
