Re: [AMBER] Cartesian restraints on Production phase

From: David A Case <david.case.rutgers.edu>
Date: Tue, 8 Sep 2020 14:18:28 -0400

On Tue, Sep 08, 2020, Lucas Santos Chitolina wrote:
>
>I am struggling to apply Cartesian restraints on some residues through
>pmemd.cuda;
>at some point my runs (100ns divided into 10 steps) crash if I try a
>"restraint_wt"
>value higher than 1.0 kcal/mol. I wish to try values higher than 10.0
>kcal/mol.

Some possible comments:

1. Do you need really high restraints? Restraining every atom in a
bunch of residues with a weight of 10 should prevent motions larger than
about 0.1 -- do you really need things tighter than this?

2. More likely related to the problem: using restraints in conjunction
with constant pressure can be problematic. Be sure to check if you are
seeing any significant volume changes, especially when things go bad.
Can you try a constant volume (test) run to see if the problem goes
away?

3. Visualization of what is going on when things go south is often very
helpful.

...good luck...dac


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Received on Tue Sep 08 2020 - 11:30:02 PDT
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