Re: [AMBER] minimization using restrain weight

From: David A Case <>
Date: Wed, 16 Oct 2019 10:56:53 -0400

On Wed, Oct 16, 2019, Debarati DasGupta wrote:
>When we apply restraint_WT = 500 in our (input) , does that apply
>for the internal coordinates?

No: the ntr=1 restraints are on the difference between the Cartesian
(xyz) coordinates in the actual structure and those in whatever file you
assigned to the "-ref" flag when you invoked sander or pmemd.
>Like when we restrain a molecule, will the x,yz coordinates of the
>molecule change after minimization?

It depends on whether the starting coordinates (given by the "-c" flag)
are the same as or different from the reference coordinates (given by the
"ref" flag.) Setting ntr=1 sets up a bias towards moving the starting
coordinates toward the reference ones.

....hope this helps...dac

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Received on Wed Oct 16 2019 - 08:00:03 PDT
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