Re: [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded

From: David A Case <>
Date: Tue, 28 May 2019 07:45:22 -0400

On Tue, May 28, 2019, Saikat Dutta chowdhury wrote:

>I am trying to simulate a homopolypeptide of a modified amino acid in
>explicit condition.
>vlimit exceeded for step 7094; vmax = 21.7545

You should visualize your trajectory to see if there in anything obvious
happening. Try running 7000 steps, then examine the restart file
(using, say the "check" option in cpptraj.) Look at the mdout file for
any clues for what is going wrong. Most likely candidate is a short
contact, usually involving a hydrogen atom. Is your temperature indeed
very low, as you gave a low target temperature?

In doing the re-run, be sure to turn on SHAKE: that is required for all
Amber rigid water molecules.

Basically, you will need to do some debugging. It may help (if you did
not already do this) to use gaff2 to build the force field: it doesn't
have any hydrogens with zero Lennard-Jones parameters, so if you problem
is a bad hydrogen contact, that may help.

...good luck...dac

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Received on Tue May 28 2019 - 05:00:03 PDT
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