AMBER Archive (2008)

Subject: Re: AMBER: output file format in SANDER.MPI & PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Aug 28 2008 - 07:34:44 CDT

Fatima -
I don't understand. Are you saying that you do two long umbrella sampling
runs and get a slightly different result? That would probably be expected,
even if you used the same software, but due to differences in rounding
errors in different algorithms, could be higher in sander vs. pmemd.
Somebody more familiar with the details of umbrella sampling may want to
comment on this...
Regards - Bob Duke
----- Original Message -----
From: <fatima.chami_at_durham.ac.uk>
To: <amber_at_scripps.edu>
Sent: Thursday, August 28, 2008 6:47 AM
Subject: AMBER: output file format in SANDER.MPI & PMEMD

> Dear All,
>
> I run Umbrella sampling simulation in both SANDER.MPI and PMEMD. I
> realized that
> the values of the restraint are different (diff. range 0.05 - 1.00)
> although the
> simulation system is literally the same.
>
> I suspect this to be inherent to SANDER and PMEMD numerical implementation
>
> best wishes
> Fatima
>
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