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

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Aug 01 2018 - 06:53:18 CDT

Sorry, yes you are correct, that should be "sum of the square of the
errors".

Are you using the standard deviation or the standard error? The latter is
more difficult to calculate but almost certainly smaller (unless your
effective sample size is abysmal). Nonetheless, I believe this has always
been considered one of the drawbacks to MM/GBSA-type methods. That and the
accurate inclusion (or lack thereof) of entropic effects.

On Wed, Aug 1, 2018 at 6:40 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> "the error is square additive, however, so you would take the square root
> of the sum of the errors when re-combining"
>
> May I ask whether the above "sum of the errors" is a shortage for the "sum
> of the square of the errors" ? If so, translating to a different albeit
> related case, let me show some data (kcal/mol) from MM-GBSA rather than FEP
> for the same system, so that /\A below should be understood as /\POTENTIAL
> from NAMD plot/xmgrace
>
> complex: -6335.08 with Stdev 64.24
>
> receptor: -6358.87 with Stdev 63.93
>
> ligand: 48.33 with Stdev 6.2
>
>
> /\Abind = complex - receptor - ligand = -24.5 with Stdev 91
>
> if the propagation of errors is treated here correctly, the whole is quite
> disappointing.
>
> Thanks a lot for checking
>
> francesco
>
>
>
>
> On Tue, Apr 10, 2018 at 2:56 PM Brian Radak <brian.radak_at_gmail.com> wrote:
>
>> 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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