Re: New NAMD version 2011-03-03 uses

From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 15 2011 - 13:18:56 CDT

Chipot's best suited to answer the first half of your question
regarding parseFEP.

But regarding NAMD:
Let's refer to your latter description as "double wide sampling".
Automated doublewide sampling in NAMD isn't available yet,
and unfortunately won't be in the upcoming 2.8 release, :(
but is something I hope to offer with the 2.9 release with some needed
infrastructural changes to make it happen smoothly. :)

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 217-244-1733
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Jeff Wereszczynski <jmweresz_at_gmail.com> writes:
> Date: Tue, 15 Mar 2011 09:49:28 -0700
> From: Jeff Wereszczynski <jmweresz_at_gmail.com>
> To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
> Subject: Re: namd-l: New NAMD version 2011-03-03 uses
> 
> Hi Chris,
> 
> These seem like some nice tools!
> 
> Not to hijack this thread, but I noticed this ParseFEP included a
> reference to "bidirectional FEP."  By this do you mean actually
> running the simulations at a given lambda value twice, once with the
> work functions calculated to the next window and once to the previous,
> or can NAMD now calculate both the forward and reverse work functions
> simultaneously?  The latter would be ideal.
> 
> Thanks,
> Jeff
> 
> 2011/3/15 Chris Chipot <chipot_at_ks.uiuc.edu>:
> > 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 ΔU values during the simulation (to
> >> obtain an idea of the probability distribtions P(ΔU) 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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