Re: New NAMD version 2011-03-03 uses

From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Tue Mar 15 2011 - 10:00:17 CDT

Christian,

please, check http://www.ks.uiuc.edu/Research/vmd/plugins/parsefep/,
which should do exactly what you need. ParseFEP
is part of the new version of VMD.

Cheers,

Chris Chipot

On 3/15/11 9:52 AM, Christian Jorgensen wrote:
> Hi all,
> I have the new NAMD version from 2011-03-03 and was wondering
> if someone could briefly outline if there are any major changes
> to the necessary input file used (e.g. variable name changes)?
>
> I am specifically interested in the free energy perturbation formalism.
> I have done some runs with the new version using the following input
>
> # FEP
> source ./fep.tcl
> alch on
> alchType fep
> alchFile system.fep
> alchCol B
> alchOutFile out.fepout_1
> alchOutFreq 500
>
> alchVdwLambdaEnd 1.0
> alchElecLambdaStart 0.5
> alchVdwShiftCoeff 5.0
> alchDecouple yes
>
> alchEquilSteps 37500 ; # 75ps
> set nSteps 75000 ; # 150ps
>
> runFEP 0.0 1.0 0.0625 $nSteps ; # 10 windows outward
>
>
> Also, I am interested in whether there have been developments
> in how namd can deal with the error analysis of the simulation.
> Is there a way of outputting ÄU values during the simulation (to
> obtain an idea of the probability distribtions P(ÄU) of the simulation)?
> Ultimately I wish to obtain an estimate of the simulation bias.
>
> Thank you for any input here
> Christian
_______________________________________________________________________

Chris Chipot, Ph.D.
Theoretical and Computational Biophysics Group
Beckman Institute
University of Illinois at Urbana-Champaign
405 North Mathews Phone: (217) 244-5711
Urbana, Illinois 61801 Fax: (217) 244-6078

                             E-mail: chipot_at_ks.uiuc.edu
                                     Christophe.Chipot_at_edam.uhp-nancy.fr
                             Web: http://www.ks.uiuc.edu/~chipot
                                     http://www.edam.uhp-nancy.fr

The light shines in the darkness, and the darkness has not overcome it.
                                                               John 1:5.
_______________________________________________________________________

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