Re: [AMBER] Error and sudden halt in equilibration

From: Bill Ross <>
Date: Thu, 21 Feb 2019 03:32:19 -0800

Are there any atom types in this ligand that wasn't in the previous ones?

In any case,  you could rerun with ntpr = 1, ntwx = 1, and see if you
see a message involving GMAX or similar and a pair of atom numbers,
indicating the model part of the problem, assuming you equilibrated
properly. Also you could try running serial, to verify whether MPI could
be the culprit.


On 2/21/19 3:00 AM, senal dinuka wrote:
> Dear AMBER users,
> 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
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> I have searched for a cause and it was reported in an earlier thread that
> it could be due to presence of bad contacts. Though I ran sufficient amount
> of minimization (GMAX = 60) I dont assume it was the cause because I was
> able to run the heating without any issue, again using the pmemd.MPI
> module. Pointing out the fact that I was able to run the same scripts
> through other 3 models, I appreciate any comments and information on this
> error and any possible ways to overcome.
> Ps. I did try starting using a different seed as suggested previously
> (irest=1) though it did not help. And if possible I wish to continue the
> same run from the heated system.
> Thank you. Regards,
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Received on Thu Feb 21 2019 - 04:00:02 PST
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