Re: [AMBER] Error and sudden halt in equilibration

From: David A Case <>
Date: Thu, 21 Feb 2019 08:22:24 -0500

On Thu, Feb 21, 2019, senal dinuka wrote:
>I am running an equilibration on a preheated system of 696 residues in 14A
>TIP3P waterbox. I did ran 3 MD production runs for same enzyme model with 3
>different ligands successfully and this is the 4th ligand-enzyme complex. I
>was brought up with the following error on equilibration using pmemd.MPI
>module of amber16 version for a 1ns.
>mpirun -np 8 pmemd.MPI
>vlimit exceeded for step 25426; vmax = 42.1209
>vlimit exceeded for step 25427; vmax = 26.3270
>vlimit exceeded for step 25434; vmax = 61.5112

One thing that is certainly possible is that there is something
different about the force field you use for the 4th ligand. Check to
see if you have hydrogens with zero Lennard-Jones parameters: these can
undergo fluctuations that put the hydrogen very close to some other
atom, leading to gigantic forces and the behavior you report above.

But this is of course a guess: how did you build your ligand library?
Is there anything different in the chemistry of the various ligands?

You might also want to save a restart file right before the system blows
up, and examine it (say, visually) for bad contacts or other problems.

...good luck....dac

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Received on Thu Feb 21 2019 - 05:30:01 PST
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