From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Jun 22 2016 - 09:49:31 CDT
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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