From: Chris Harrison (charris5_at_gmail.com)
Date: Tue Mar 15 2011 - 10:48:04 CDT
For the NAMD input for FEP, no user commands have changed since release
For error analysis, as Chipot suggested, the ParseFEP plugin is your
best solution at present. Automated analysis in NAMD won't be available
until some later release; sometime after release of 2.8.
-- 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 Chris Chipot <chipot_at_ks.uiuc.edu> writes: > Date: Tue, 15 Mar 2011 10:00:17 -0500 > From: Chris Chipot <chipot_at_ks.uiuc.edu> > To: Christian Jorgensen <christian.jorgensen_at_merton.ox.ac.uk> > CC: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> > Subject: Re: namd-l: New NAMD version 2011-03-03 uses > User-Agent: Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; > rv:188.8.131.52) Gecko/20110303 Thunderbird/3.1.9 > > 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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