Re: Applying "selectionRule" in Multiple Walker ABF

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Tue May 31 2016 - 01:27:08 CDT

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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