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

From: Robert Duke <rduke.email.unc.edu>
Date: Thu, 28 Aug 2008 08:34:44 -0400

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.durham.ac.uk>
To: <amber.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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Sun Aug 31 2008 - 06:07:30 PDT
Custom Search