The initial energy/forces are HUGE. I would not expect a good outcome.
I suggest looking at the initial structure and trying to see why there is
such high energy, particularly around the atom listed for the GMAX above
the energy details. the VDW energy gets reduced by step 1000, but the bond
energy has gone up a lot, and I would worry that the initial energy was
enough to cause problems in the structure.
On Fri, Dec 18, 2020 at 4:19 PM Aanshi Gandhi <
aanshi.gandhi.mail.utoronto.ca> wrote:
> Sorry when I said "allowed to run for 10 hours" I was referring to the
> #SBATCH --time=D-HH:MM line in my submission script. So in the script I
> sent the time was set for 3h 30 mins but in the past I have tried setting
> it for 10 hours as well.
>
> In terms of the output file, it seems to stop writing after nstep 1000
> (attached here as well), would this be a problem with my structure? Or
> should I change the parameters in minimization to fix this?
>
> Thank you,
> Aanshi Gandhi (she/her)
> M.ASc Candidate, Garton Lab
> Email <mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn <
> https://www.linkedin.com/in/aanshigandhi/>
>
>
>
> On 2020-12-18, 4:10 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
> wrote:
>
> EXTERNAL EMAIL:
>
> I don't understand what you mean. The slurm message says that it was
> killed
> due to time limit. I'm not sure how it could run longer unless the
> limit
> were changed.
> It's possible that something is wrong in the minimization and it is no
> longer proceeding, but you would need to look at your output file to
> know
> that. I suggest checking occasionally during minimization to see if it
> is
> writing more data.
>
> On Fri, Dec 18, 2020 at 3:59 PM Aanshi Gandhi <
> aanshi.gandhi.mail.utoronto.ca> wrote:
>
> > Hi Carlos,
> >
> > I've tried previous runs where I've allowed the minimization to run
> for 10
> > hours and it still gave me the same error.
> >
> > Thank you,
> > Aanshi Gandhi (she/her)
> > M.ASc Candidate, Garton Lab
> > Email <mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn <
> > https://www.linkedin.com/in/aanshigandhi/>
> >
> >
> >
> > On 2020-12-18, 3:46 PM, "Carlos Simmerling" <
> carlos.simmerling.gmail.com>
> > wrote:
> >
> > EXTERNAL EMAIL:
> >
> > the slurm time limit is set by your system administrator, not
> inside
> > Amber.
> > it looks like it ran for about 3.5 hours before being killed.
> you might
> > want to check to see if there is a different queue where you can
> run
> > longer
> > jobs. You can reduce the number of minimization steps to get
> this to
> > work,
> > but it will be hard to get your later MD jobs finished in that
> amount
> > of
> > time.
> >
> >
> > On Fri, Dec 18, 2020 at 3:40 PM Aanshi Gandhi <
> > aanshi.gandhi.mail.utoronto.ca> wrote:
> >
> > > Hello!
> > >
> > > I am trying to run a minimization on a protein using sander on
> a
> > Compute
> > > Canada cluster (beluga to be specific). I have attached my two
> > minimization
> > > input files (one for water & ions restrained [HC1_minwat.in]
> and one
> > for
> > > the entire protein [HC1_minall.in] and my submission script
> > > (submit_min.sh). When running this minimization, I get the
> following
> > error:
> > > “Starting MD Minimization at: Fri Dec 18 13:26:34 EST 2020
> > > slurmstepd: error: *** JOB 14510696 ON blg5805 CANCELLED AT
> > > 2020-12-18T18:56:06 DUE TO TIME LIMIT ***”. I have tried
> changing
> > various
> > > parameters in all my files based on previous email forums and
> the
> > Amber
> > > 2020 manual to no avail. If anyone has any ideas or
> suggestions, I
> > would
> > > greatly appreciate it.
> > >
> > > Thank you,
> > > Aanshi Gandhi (she/her)
> > > M.ASc Candidate, Garton Lab
> > > Email<mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn<
> > > https://www.linkedin.com/in/aanshigandhi/>
> > >
> > >
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Received on Fri Dec 18 2020 - 13:30:03 PST
