Re: ParseFEP error with FEP in segments at different lambda schedule

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Apr 10 2018 - 07:56:40 CDT

The simple solution to this is to break the simulations into two groups
where the spacings are identical. So long as you get the directions correct
the net free energy is just the sum of the two. Most people probably know
this, but just to be complete, the error is square additive, however, so
you would take the square root of the sum of the errors when re-combining.

HTH,
BKR

On Sun, Apr 8, 2018 at 9:58 AM, Chris Chipot <chipot_at_ks.uiuc.edu> wrote:

> Francesco,
>
> ParseFEP assumes constant ∆λ throughout the free-energy calculations.
>
> Cheers,
>
> Chris Chipot
>
>
>
> On 4/8/18 3:46 PM, Francesco Pietra wrote:
>
> Hello:
> I carried out FEP for Unbound ligand in water along two segments, as
> follows:
>
> frwd-01
> 0.00 0.20 0.05 $numSteps
>
> frwd-02
> 0.20 1.00 0.10 $numSteps
>
> back-01
> 1.00 0.80 -0.05 $numSteps
>
> back-02
> 0.80 0.00 -0.10 $numSteps
>
> concatenating the results as follows:
> frwd-01.fepout > frwd.fepout
> frwd-02.fepout >> frwd.fepout
>
> back-01.fepout > back.fepout
> back-02.fepout >> back.fepout
>
> ParseFEP with SOS estimator gave error:
>
>> domain error: argument not in valid range
>> domain error: argument not in valid range
>> while executing
>> "expr {$mean/$nfepdata}"
>> (procedure "::ParseFEP::analysis_normal_result" line 5)
>> invoked from within
>> "::ParseFEP::analysis_normal_result $window $fororback $nfepdata
>> $fepdata"
>> (procedure "::ParseFEP::normal_parse_log" line 39)
>> invoked from within
>> "::ParseFEP::normal_parse_log $::ParseFEP::fepbofile backward "
>> (procedure "namdparse" line 36)
>> invoked from within
>> "namdparse"
>> (in namespace inscope "::ParseFEP" script line 16)
>> invoked from within
>> "::namespace inscope ::ParseFEP {
>>
>> if { [string length $::ParseFEP::fepofile] < 1 && [string length
>> $::ParseFEP::fepdwfile] < 1} {
>> ..."
>> 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)
>>
>
> ParseFEP with BAR gave no error, but only partial output and no graphics.
>
> If I understand, the lambda schedule that I choose is incorrect for the
> plugin.
>
> Previously I carried out successfully the same FEP along four sectors,
> with same /\lambda throughout. Now, in view of heavy FEP with the complex
> ligand-protein, I wanted to use tight /\lambda for the steep regions only,
> apparently with a wrong protocol.
>
> Thanks for advice
>
> francesco pietra
>
>
>
>
> --
>
> Chris Chipot
> CNRS research director, University of Lorraine
> Adjunct professor of physics, University of Illinois, Urbana-Champaign
>
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> Theoretical and Computational Biophysics Group
> 3165 Beckman Institute for Advanced Science and Technology
> University of Illinois at Urbana-Champaign
> 405 North Mathews
> Urbana, Illinois 61801 Phone: (217) 300-0380
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_Univ-Lorraine.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.lia-uiuc.cnrs.fr
>
> It is hard for France to maintain a thirty-five-hour workweek when
> China and India have invented a thirty-five-hour workday.
> Thomas L. Friedman
> _______________________________________________________________________
>
>

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