Hi Rebecca,
Is this problem occurring with pmemd or pmemd.cuda or with sander?
Can you also share what commands you are using in the input file to output
to tje trace files?
On Fri, Feb 14, 2020, 7:34 AM Rebecca Twidale <rebecca.twidale.bristol.ac.uk>
wrote:
> Dear AMBER users,
>
>
>
> I was just wondering if anyone has experience with running umbrella
> sampling on a dihedral angle in either AMBER16 or AMBER18? I’m currently
> trying to do just that and I’m having problems with what is being written
> to the trace file. I’m stepping from 60 degrees to 180 degrees, and my r1
> and r4 values are minus and plus 180 degrees respectively in each rc
> window. For the majority of RC windows, it just outputs 0 to the trace
> file, but otherwise, it outputs the value I would expect to the trace file.
> There does not seem to be any pattern to when it correctly writes the
> restraint values to the trace file.
>
>
>
> My restraint file is as below:
>
>
>
> &rst
>
> iat=3969,3971,3972,3973,
>
> r1=-120.0, r2=60.0, r3=60.0, r4=240.0,
>
> rk2=100, rk3=100,
>
> /
>
>
>
> I have attempted to run the same simulation in AMBER14, 16 and 18. The
> problem only occurs in AMBER16 and AMBER18. Unfortunately I cannot get
> around the issue by using AMBER14 because I am using DFTB3, which is not
> available in AMBER14.
>
>
>
> Do you know if this is a known problem for the later versions of Amber and
> if there is a way to fix this problem?
>
>
>
> Best wishes,
>
> Rebecca
>
> -------
> Rebecca Twidale
>
> TMCS PhD Student
> Mulholland Research Group
> Centre for Computational Chemistry
> School of Chemistry - University of Bristol
> Bristol BS8 1TS - United Kingdom
>
>
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>
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Received on Fri Feb 14 2020 - 19:30:01 PST
