Re: [AMBER] Reproduce a Simulation

From: Skanda Sastry via AMBER <>
Date: Thu, 30 Nov 2023 20:16:02 -0800

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.


On Thu, Nov 30, 2023 at 6:20 PM Xuebin Feng via AMBER <>

> 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 mailing list
Received on Thu Nov 30 2023 - 20:30:02 PST
Custom Search