Re: [AMBER] minimizing a pyridine in water

From: David A Case <>
Date: Sat, 25 Apr 2020 13:29:12 -0400

On Sat, Apr 25, 2020, Debarati DasGupta wrote:

>I am trying to minimize a 1P3 molecule in TIP3P water and this is my input file
>Initial Minimization on Whole System
> imin = 1,
> igb = 0,
> cut = 12,
> ntmin = 2,
>maxcyc = 2000,
> ntb = 1,
>ntr = 1, restraintmask = ':1P3', restraint_WT = 10,
>I am using sander.MPI on 12 processors to run this minimization step...

First, Make sure that you have examined the output file from the run you
already have to look for problems that may have been reported there.

If that doesn't help, run on serial sander, and see what happens. If that
works, try sander.MPI with something like 4 threads: it's possible
that your system is so small that something bad is happening with 12
threads. (It still should not segfault).

I don't know how many waters you have, but my guess is that (especially
using cut=12) that you may simply have a case where your cutoff is too
big, and you are missing the error message telling you that.

...good luck...dac

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Received on Sat Apr 25 2020 - 10:30:02 PDT
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