From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Tue Mar 15 2011 - 17:37:15 CDT
Hi Jeff,
in its current form, ParseFEP expects you to feed it an *fepout*
file for the forward simulation and possibly a second *fepout*
file for the backward transformation, in which case, you can
request a simple-overlap sampling (SOS) or a Bennett
acceptance ratio (BAR) estimator of the free energy. I
am inclined to advocate to use the latter, which is the
maximum-likelihood estimator. It should also yield the
smallest variance (see our Good Practices paper, J. Phys.
Chem. B 2010, 114,10235--10253).
Ideally, one would like to have a single file containing the
free-energy changes for both the to + and the to
- transformations generated from a single FEP run,
i.e. a double-wide sampling calculation. As Chris Harrison
pointed out, this is not yet implemented in NAMD, though
we hope to have it available in the near future. The only
advantage to have an effective implementation of the
double-wide sampling algorithm is to make the concurrent
estimation of the forward and backward free-energy changes
appreciably cheaper than two individual calculations would be.
Hence, for now, please, organize your bidirectional calculations
in two runs, one from 0 to 1 and the other from 1 to 0. One
last, trivial comment. The rewriting of the potential energy
function with a soft-core term removes the linearity of the
former in . As a result, the result of a backward simulation
can no longer be inferred from the sole knowledge of the
forward transformation. The forward and the backward
free-energy changes must be determined separately.
Cheers,
Chris Chipot
On 3/15/11 11:49 AM, Jeff Wereszczynski wrote:
> 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 U values during the simulation (to
>>> obtain an idea of the probability distribtions P(U) 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.
>> _______________________________________________________________________
>>
>>
--
_______________________________________________________________________
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.
_______________________________________________________________________
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:19:56 CST