From: Chris Chipot (chipot_at_ks.uiuc.edu)
Date: Thu Mar 17 2011 - 13:09:30 CDT
Hi Christian,
parseFEP assumes that the backward fepout file is the mirror image of the
forward fepout file, i.e. if in your forward file, you ran from λ = 0 to
0.2, then
the backward file should range from λ = 0.2 to 0. It also assumes that your
increment, δλ, is the same for the forward and backward transformations.
Cheers,
Chris Chipot
On 3/17/11 12:58 PM, Christian Jorgensen wrote:
> Hi all,
>
> when using ParseFEP with a fepout file for the forward and the backward run
> I keep encountering a domain error of the form
>
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr sqrt($instant_error_gauss)"
> (procedure "::ParseFEP::FEP_formula" line 361)
> invoked from within
> "::ParseFEP::FEP_formula $file $file_entropy $file_lambda $window $mean_xi $fororback"
> (procedure "::ParseFEP::normal_parse_log" line 60)
> invoked from within
> "::ParseFEP::normal_parse_log $::ParseFEP::fepofile forward"
> (procedure "::ParseFEP::namdparse" line 172)
> invoked from within
> "::ParseFEP::namdparse"
> (in namespace inscope "::ParseFEP" script line 21)
> invoked from within
> "::namespace inscope ::ParseFEP {
> ##if {$::ParseFEP::fepbofile != ""} {set ::ParseFEP::sosindex 1 }
>
> if { [string length $fepofile]< 1 } {
> tk_dial..."
> invoked from within
> ".parseFEP.runbutton invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .parseFEP.runbutton"
> (command bound to event)
>
>
>
> Does this invalid argument arising when calculating sqrt($instant_error_gauss) occur because $instant_error_gauss is taking values<0?
> I believe it is causing me issues because the ParseFEP log file stops at λ=0.5
>
>
>
> #=================================================
> # Free energy perturbation
> # --------------------------------
> #forward/backward λ ∆∆A ∆A δε
> #
> #-------------------------------------------------
> forward: 0.0000 0.0000 0.0000 0.0000
> forward: 0.1000 -0.9392 -0.9392 0.0506
> forward: 0.2000 -0.8597 -1.7989 0.1287
> forward: 0.3000 -0.5557 -2.3547 0.1357
> forward: 0.4000 -0.5542 -2.9089 0.1381
> forward: 0.5000 -0.4808 -3.3897 0.1421
>
>
> Any input here would be really helpful
> thanks
> Christian
>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Chris Chipot [chipot_at_ks.uiuc.edu]
> Sent: Tuesday, March 15, 2011 10:37 PM
> To: Jeff Wereszczynski
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: New NAMD version 2011-03-03 uses
>
> 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 λ to λ + δλ and the λ to
> λ - δλ 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 λ. 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><mailto: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<mailto:chipot_at_ks.uiuc.edu>
> Christophe.Chipot_at_edam.uhp-nancy.fr<mailto: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<mailto:chipot_at_ks.uiuc.edu>
> Christophe.Chipot_at_edam.uhp-nancy.fr<mailto: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.
_______________________________________________________________________
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