**From:** Francesco Pietra (*chiendarret_at_gmail.com*)

**Date:** Wed Aug 01 2018 - 09:10:54 CDT

**Next message:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Previous message:**Gerard Rowe: "SegFault in QM/MM run"**In reply to:**Brian Radak: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Next in thread:**Francesco Pietra: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Reply:**Francesco Pietra: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Standard deviation, as provided by xmgrace when loading the .agr file

created with NAMD plot.

Could xmgrace, or other software, be turned to calculate the standard

error? I am dealing with very long trajectories, so that hand calculation

is hardly feasible. On the other hand, in comparison of different poses for

the same ligand and receptor, MM-GBSA could be of some utility. Otherwise,

could you provide a link to how implementing entropy with MM-GBSA?

I turned to MM-GBSA while attempting to improve on absolute FEP. Nearly

perfect frwd+back "probability" superimposition proved not enough: I

obtained large scatter of /\A for the 0.8-1.0 sector (the one on which I am

now focusing the attention) on change of flags that should be irrelevant if

quasi converge had been reached. I am now waiting results for FEP at the

limit of what can be done in a 24hr run for 0.8-1.0 on my cluster (number

of windows/number of FEP steps, ts=2fs, while I used before ts=1.0 fs). For

a system of biological interest I am faced by such a high wall. In other

quarters, absolute FEP is carried out on GPUs (none of them on my cluster),

so that the "wall" should be much lower than with CPUs. But, was the

CPU/GPU comparison well tested?

Thanks for advice

francesco

On Wed, Aug 1, 2018 at 1:53 PM Brian Radak <brian.radak_at_gmail.com> wrote:

*> 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
*

*>>>> _______________________________________________________________________
*

*>>>>
*

*>>>>
*

*>>>
*

*>
*

**Next message:**Josep Ivan Balaguer Molins: "Re: Problems with temperature control."**Previous message:**Gerard Rowe: "SegFault in QM/MM run"**In reply to:**Brian Radak: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Next in thread:**Francesco Pietra: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Reply:**Francesco Pietra: "Re: ParseFEP error with FEP in segments at different lambda schedule"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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