Re: [AMBER] Minimization of ethanol in water

From: David Case <>
Date: Wed, 6 Nov 2019 22:25:17 +0000

On Wed, Nov 06, 2019, Debarati DasGupta wrote:

>Trying to do TI setup for an ethanol molecule in water…

>I am still getting my output files generated but my slurm.out file has
>this big page of errors… ANYTHING wrong that I am doing?

Run a *short* simulation with pmemd (not pmemd.MPI). Don't use slurm
(if possible): just run a minute or so in interactive mode. It's not
even clear from what you wrote which step is running when you get the

If the error seems gone, switch to pmemd.MPI -- again just a few steps,
avoiding any queueing system.

>*** Error in `/usr/local/amber18/bin/pmemd.MPI': corrupted size vs. prev_size: 0x00000000024e89a0 ***

I don't recognize this error, for whatever that might be worth :=)


AMBER mailing list
Received on Wed Nov 06 2019 - 14:30:01 PST
Custom Search