Date: Sat, 25 Apr 2020 15:38:29 +0000
Hi Prof Simmerling,
When I redid the job on a single processor, there was no error message! Strange, but Now I have a new hassle.
The slurm.out file says no error as seen in this pic, even when I open the allmin.out file generated, its stagnated at Nsteps= 750 and this is what I shown in the last 5 lines of the output generated, it just appears choked somewhere. The slurm DB shows this job is running still...
Thanks
Debarati
Output file last few lines:
[cid:image002.png.01D61AF5.4A4E8D60]
Slurm.out file contents :
[cid:image001.png.01D61AF3.FCC0FED0]
From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 25 April 2020 09:19
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] minimizing a pyridine in water
I find it helpful to run the non-mpi one to see better error messages.
On Sat, Apr 25, 2020, 9:11 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Hi everyone
> I am trying to minimize a 1P3 molecule in TIP3P water and this is my input
> file
>
> Initial Minimization on Whole System
> &cntrl
> 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...
>
> I get this 1 page error, most of which I am unable to decipher
>
> [cid:image001.png.01D61AE1.5EA78910]
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(image/png attachment: 3773FE3BF4C54F60BCB59D486053AC12.png)
(image/png attachment: 7227E9CEB21B4408A03381096B88A082.png)
