Also, if you simply just want to save the 70 ns to 80 ns interval, you
don't have to rerun the simulation, you can just use the cpptraj trajin to
read only the frames corresponding to 70ns to 80ns, then use trajout to
write that segment to a new trajectory file.
On Thu, Nov 30, 2023 at 8:16 PM Skanda Sastry <skandasastry.gmail.com>
wrote:
> It should be in the first 100 lines in the out file (whatever file you
> denoted after the *-o* flag in pmemd.cuda). The statement says "Note:
> Setting random seed to ____ based on wallclock time...". Say the file name
> is "prod.out", you can use the command
>
> cat prod.out | grep "Note:"
>
> to find the seed.
>
> HTH,
> Skanda
>
>
> On Thu, Nov 30, 2023 at 6:20 PM Xuebin Feng via AMBER <amber.ambermd.org>
> wrote:
>
>> Dear AMBER Community,
>>
>> I am trying to reproduce the 70 ns to 80 ns interval of a 100 ns
>> simulation and write trajectory in a smaller interval. I am not sure how to
>> specify the restart point saved at 70 ns as the starting point of the new
>> simulation, and I am also not sure where I can find the random seed used in
>> the previous simulation (I used ig = -1 in the previous simulation, but I
>> think the random seed should be stored somewhere). Can anyone help me with
>> this problem. Thanks so much!
>>
>> Sincerely,
>>
>> Xuebin Feng
>> 4th-Year PhD Student at University of Toronto
>> Department of Chemical Engineering and Applied Chemistry
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Nov 30 2023 - 20:30:02 PST
