From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Thu Jun 23 2016 - 03:07:13 CDT
Thanks sir, for your reply. I will always opt for better sampling all over
the phase space.
Souvik
On Wed, Jun 22, 2016 at 9:30 PM, Marlon Sidore <marlon.sidore_at_gmail.com>
wrote:
> 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
>>
>>
>
-- Souvik Sinha Research Fellow Bioinformatics Centre (SGD LAB) Bose Institute Contact: 033 25693275
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