Yes, that is the step. But I am sorry for not bing clear at first, I am using my own system instead of Sustiva-RT complex. My HPC allows jobs to run for 24 hrs.
And I am performing minimization for 2000 steps but the last step I can see in output file is 1057 before it is terminated my HPC’s job scheduler.
Can I just go ahead and use the existing .ncrst file for MD run?
Thank you.
——
> On Oct 5, 2020, at 11:38 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> can you be more specific on which step you mean, and the length of the wall
> clock limit?
> If you mean the step "Minimize and Equilibrate the Sustiva-RT complex",
> this should not take very long and you may want to check your output to see
> if it is actually running. For debugging you might want to set ntpr=1 (but
> do not do this for production runs).
>
> On Mon, Oct 5, 2020 at 11:29 AM Jatin Kashyap <jk435.njit.edu> wrote:
>
>> Dear AMBER Community,
>>
>> I am following the antechamber tutorial for my system (
>> https://ambermd.org/tutorials/basic/tutorial4b/index.html).
>> During the minimization step, the wall clock limit was hit before
>> completion of the minimization.
>> Shall it affect the structure of output files, and prevents me from going
>> to next step i.e., equilibration.
>> Do I have to restart the minimization by decreasing the minimization steps
>> so that it will be finished before hitting the wall limit OR I don’t have
>> to worry about it, and I can continue with existing files, if yes then how?
>>
>> Thank you.
>>
>>
>> ——
>> Jatin Kashyap
>> Ph.D. Student
>> Dr. Dibakar Datta Group
>> Department of Mechanical and Industrial Engineering
>> New Jersey Institute of Technology (NJIT)
>> University Heights
>> Newark, NJ 07102-1982
>> Phone- (201)889-5783
>> Email- jk435.njit.edu
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Oct 05 2020 - 09:30:03 PDT
