Re: [AMBER] Restraint ramp

From: David Case <>
Date: Sun, 18 Aug 2019 01:16:40 +0000

On Sun, Aug 18, 2019, Dhananjay wrote:
>I am relatively new to the use of restraints in the MD simulation.
>Similar to temperature ramp to heat the system, I am trying to apply
>restraint ramp to restraint positions of protein atoms only

The restraintmask variable applies to harmonic constraints that keep atoms in
the restraintmask close to the distances they have in the reference structure
(specified by the -ref flag).

>I want to increase the restraint on the positions of the proteins

Amber does not offer any automated way to do this.

> &wt TYPE='REST', istep1=0, istep2=250000,
> value1=0.0, value2=1.0, /

The "restraints" referred to here are internal (aka "NMR") restraints, that
generate forces based on internal distances, angles, and so on. In spite of
the similarity in naming, this has nothing to do with coordinate restraints.

...hope this helps....dac

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Received on Sat Aug 17 2019 - 18:30:02 PDT
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