A bond passing through a ring might be such a case, requiring manual or
AI help.
Bill
On 12/18/20 1:27 PM, Carlos Simmerling wrote:
> 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 - 14:30:02 PST
