Hi Andreas,
I did minimize and equilibrate my system and then started simulating my system. Since I am trying to run 100 ns of simulation i broke it down into small steps to avoid getting NaN values, because I often get it when I try to run the whole 100ns simulation at one go.
Attached are the two production run files with exact same input but the energy values are different, and this difference is based on the random seed number, which I still don't understand why should influence my energy (I am using ntt=1). If I use the same ig number I get the exact same value, but still the system crashes with NaN.
Thanks
Roma
________________________________
From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Sent: Saturday, February 17, 2018 8:09:17 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda
Hi Roma,
did you run a minimizartion before the MD? Try minimizing with pmemd instead of pmemd.cuda. Please share your output file.
Best,
Andy
> Am 17.02.2018 um 05:07 schrieb Roma Mukhopadhyay <roma1988.nmsu.edu>:
>
> Dear all,
>
>
> I have been trying to simulate my molecule of interest using barostat=1, which uses Monte Carlo Barostat algorithm in pmemd cuda, but the simulation keeps on crashing within 0.5 ns giving NaN values for energy. However when I run the same simulation in pmemd platform it works fine. Has anyone faced the same issue?
>
>
> Is their any specific way to overcome this issue in pmemd cuda platform? I have seen if I use Berendsen algorithm this problem does not arise at all.
>
>
> Any and all help is highly appreciated.
>
>
> Thanks
>
> Roma
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Received on Sat Feb 17 2018 - 09:00:03 PST
