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.
Bill
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
