Re: Applying "selectionRule" in Multiple Walker ABF

From: Marlon Sidore (marlon.sidore_at_gmail.com)
Date: Wed Jun 22 2016 - 11:00:32 CDT

Hello,

I would also be interested in using the multiple walker ABF with multiple
transition coordinates (2D or 3D). How easy would it be ?

Marlon

Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France

2016-06-22 16:49 GMT+02:00 Jeff Comer <jeffcomer_at_gmail.com>:

> Dear Souvik Sinha,
>
> Sorry for not replying for so long. Justice delayed is probably justice
> denied.
>
> First, the error you that you saw in your first post is because $cMax
> == 0. You can probably check for that and not apply selection rules
> when that is case.
>
> You are completely right about the 2D ABF issue! I didn't set up the
> selection rules to work with 2D transition coordinates.
> colvarbias_abf::bin_count() and colvarbias_abf::current_bin() only
> refer to the first dimension. It looks to me that it might not be that
> hard to extend it to the second dimension. If you're still interested
> I think I can fix this.
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
> Website: http://jeffcomer.us
>
>
> On Tue, May 31, 2016 at 1:27 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
> wrote:
> > Hi,
> >
> > For the Multiple-walker ABF, I have followed the scripts provided in the
> > article “Multiple-Replica Strategies for Free-Energy Calculations in
> NAMD:
> > Multiple-Walker Adaptive Biasing Force and Walker Selection Rules (J.
> Chem.
> > Theory Comput., 2014, 10 (12), pp 5276–5285) ” . For enquiring the
> reason of
> > the error I posted earlier, I did check the values of few constants of
> the
> > scripts (e.g. binNum, bin, count etc.). I don’t know whether I am right
> or
> > not, but my understanding right now is as follows:
> >
> > In the case of 2D calculation, the process “selectionRules” is
> considering
> > only the first collective variable as bin identifier of different
> walkers.
> > So, it's taking the count values only from the first bin of the second
> > collective variable correspond to any specific value of the first
> collective
> > variable. Rest of the bins of second collective variables correspond to a
> > value of the first collective variable is getting ignored. But I think,
> > “selectionRules” is applied to exchange state files in a way that all the
> > regions of the phase space would be sampled uniformly & not leaving any
> > space neglected. So now, what can be done in case of 2D?
> >
> > I may be completely wrong. Any advice would be helpful to understand the
> > situation.
> >
> > Thanks.
> >
> >
> > On Fri, May 27, 2016 at 8:13 PM, Souvik Sinha <souvik.sinha893_at_gmail.com
> >
> > wrote:
> >>
> >> Hi,
> >> I am trying to construct a 2D energy landscape using Multiple-walker ABF
> >> protocol. But the following error is showing up during application of
> >> "selectionRule".
> >>
> >> colvars: shared ABF: Sharing gradient and samples among replicas at
> step
> >> 130000
> >> TCL: domain error: argument not in valid range
> >> FATAL ERROR: domain error: argument not in valid range
> >> while executing
> >> "expr (double($cMax-$cMin))/$cMax"
> >> (procedure "selectionRules" line 30)
> >> invoked from within
> >> "selectionRules"
> >> ("for" body line 5)
> >> invoked from within
> >> "for {set i 0} {$i < $n} {incr i} {
> >> run $sharedFreq
> >> cv bias abf1 share
> >> if {$i % 50 == 49} {
> >> selectionRules
> >> }
> >> }"
> >>
> >> I think there is a problem for reading the "count" for a specific bin,
> >> though I am not sure about that. Please help me solving this.
> >>
> >> Here is part of the configuration file used for sharing between walkers:
> >>
> >> #################################################
> >>
> >> source /apps/NAMD_2.11b1_Source/lib/selectionRules.tcl
> >> source /apps/NAMD_2.11b1_Source/lib/resampleWalkers.tcl
> >> source /apps/NAMD_2.11b1_Source/lib/minExchanges.tcl
> >>
> >>
> >> firsttimestep 80000
> >> replicaUniformPatchGrids on
> >> set n 1250
> >> set sharedFreq 1000
> >> for {set i 0} {$i < $n} {incr i} {
> >> run $sharedFreq
> >> cv bias abf1 share
> >> if {$i % 50 == 49} {
> >> selectionRules
> >> }
> >> }
> >>
> >> #################################################
> >>
> >> With regards
> >> --
> >> Souvik Sinha
> >> Research Fellow
> >> Bioinformatics Centre (SGD LAB)
> >> Bose Institute
> >>
> >> Contact: 033 25693275
> >
> >
> >
> >
> > --
> > Souvik Sinha
> > Research Fellow
> > Bioinformatics Centre (SGD LAB)
> > Bose Institute
> >
> > Contact: 033 25693275
>
>

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