Re: [AMBER] nmr restraints and periodic boundary conditions

From: David A Case <>
Date: Tue, 18 Nov 2014 20:50:37 -0500

On Tue, Nov 18, 2014, Chris Moth wrote:
> 2) Do you agree that wrap_to() in pbc.F90 could be modified so that the
> "center of mass" of the tethering protein could be used to move the heme
> group along with it? Slightly Rephrased... Is there any harm in
> skipping the COM calculation of the heme group, and just wrapping it by
> using the COM of the tethering protein?

To expand on what Jason said:

I think the easiest and best solution is just to turn off wrapping. The
wrap_to() routine doesn't have the flexibility of cpptraj to control imaging:
it will work OK for a single protein in water, but not for the many more
complicated things people actually need to simulate.

We *could* add options to pmemd to make its wrapping as flexible as that in
cpptraj, but imaging (in my view) is best dealt with after the fact, not
during the trajectory itself.


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Received on Tue Nov 18 2014 - 18:00:02 PST
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