On Wed, Apr 5, 2017 at 8:11 AM, Karolina Mitusińska (Markowska) <
markowska.kar.gmail.com> wrote:
> 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?
>
pmemd, yes. pmemd.cuda, no -- you'll hit an error like this one:
http://archive.ambermd.org/201609/0273.html
It's impossible in any Amber program to use SETTLE on both CRY and WAT
residues (and since pmemd.cuda doesn't support SHAKE on multiple
constraints for a single atom, this won't work in pmemd.cuda at all).
So if you mess with residue names in a topology file, don't use that file
for simulation.
HTH,
Jason
--
Jason M. Swails
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Received on Wed Apr 05 2017 - 06:00:11 PDT
