AMBER Archive (2008)

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

From: fatima.chami_at_durham.ac.uk
Date: Thu Aug 28 2008 - 07:53:42 CDT

Quoting Robert Duke <rduke_at_email.unc.edu>:

>
> Fatima -
> I don't understand. Are you saying that you do two long umbrella sampling
> runs and get a slightly different result?
yes indeed
> 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...
This was just a test to benchmark my simulation system.
I will have to use PMEMD .

thanks
Fatima
> 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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> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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