Re: New NAMD version 2011-03-03 uses

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Mar 17 2011 - 13:53:08 CDT

Use a window increment of -0.10 for reverse runs.

Best,
Chris

On Thursday, March 17, 2011, Christian Jorgensen
<christian.jorgensen_at_merton.ox.ac.uk> wrote:
> 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
>>
>>
>> ______

-- 
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

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