From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Thu Mar 17 2011 - 13:34:44 CDT
Hi again
Thanks,
In the FEP section of the configuration file I can only go from 0.0 to 1.0:
# 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 12500 ; # 25ps
set nSteps 25000 ; # 50ps
runFEP 0.0 1.0 0.10 $nSteps ; # 10 windows outward
It is not possible to run the mirror image directly
(i.e. going from 1.0 to 0.0 is not allowed)
runFEP 1.0 0.0 0.10 $nSteps ; # 10 windows outward
as this causes a
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
ERROR: 'alchLambda' is a required configuration option
ERROR: when 'alch' is set
ERROR: alchLambda defines: Coupling parameter value
ERROR: 'alchLambda2' is a required configuration option
ERROR: when 'alch' is set
ERROR: alchLambda2 defines: Coupling comparison value
For the reverse run, instead, the way I have done it is to start
from the final mutated form and then mutated back to the initial
form still using the configuration file setup that works (i.e. 0.0 to 1.0)
# 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 12500 ; # 25ps
set nSteps 25000 ; # 50ps
runFEP 0.0 1.0 0.10 $nSteps ; # 10 windows backward
I must also stress that I get the domain error when only inputting the .fepout file
for the forward run.
I am happy to link to the .fepout file I am using
My increments are the same for forward/backward runs (0.1, 10 windows)
Christian
________________________________________
From: Chris Chipot [chipot_at_ks.uiuc.edu]
Sent: Thursday, March 17, 2011 6:09 PM
To: Christian Jorgensen
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: New NAMD version 2011-03-03 uses
Hi Christian,
parseFEP assumes that the backward fepout file is the mirror image of the
forward fepout file, i.e. if in your forward file, you ran from λ = 0 to
0.2, then
the backward file should range from λ = 0.2 to 0. It also assumes that your
increment, δλ, is the same for the forward and backward transformations.
Cheers,
Chris Chipot
On 3/17/11 12:58 PM, Christian Jorgensen wrote:
> Hi all,
>
> when using ParseFEP with a fepout file for the forward and the backward run
> I keep encountering a domain error of the form
>
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr sqrt($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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