Re: New NAMD version 2011-03-03 uses

From: Jeff Wereszczynski (jmweresz_at_gmail.com)
Date: Tue Mar 15 2011 - 11:49:28 CDT

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 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
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>
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>
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