Re: [AMBER] center of mass restraint in pmemd.cuda

From: David A Case <>
Date: Sun, 18 Mar 2018 14:52:25 -0400

On Thu, Mar 15, 2018, Rajarshi Roy wrote:
> I am trying do an umbrella sampling of nucleic acid. One of my restraint
> co-ordinate is cpd angle (pseudo- dihedral angle ), for that I need to
> restraint center of mass of four group of atoms. I am little bit confuse
> how to choose the iat value. In the manual I found that it should be
> negative, but it is not running in cuda. Here is my restraint file,

I'm pretty sure pmemd.cuda only supports COM distance restraints, and
not the corresponding angle or dihedral restraints.

Hence the "igr3" and "igr4" namelist values are not legal ones.

[Please, someone correct me if I'm wrong, or out of date here!]


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Received on Sun Mar 18 2018 - 12:00:02 PDT
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