[AMBER] Error and sudden halt in equilibration

From: senal dinuka <senal.ichemc.edu.lk>
Date: Thu, 21 Feb 2019 16:30:00 +0530

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,

D L Senal Dinuka
Grad.Chem., A.I.Chem.C.
Research Assistant
College of Chemical Sciences
Institute of Chemistry Ceylon
Sri Lanka
+94 77 627 4678

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Received on Thu Feb 21 2019 - 03:30:02 PST
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