From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Apr 27 2017 - 16:00:31 CDT
Hi Souvik,
Indeed, you can always find the current documentation here:
http://colvars.github.io/
Multiple-walker eABF works fine. To estimate the free energy, you can merge
CZAR results from different walkers. For that, run a single eABF simulation
for zero steps, providing the output from all walkers as inputPrefix
<http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-590006.1.2>.
To get all the necessary input, you need to enable writeCZARwindowFile
<http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-640006.2.1>
during
your calculations (if you forgot, you can also extract this information
from state files, but that will an extra step).
The NAMD config for combining might look like this, using Tcl to build the
list of files:
set f base_name
set n_replicas 42
set input ""
for {set i 0} {$i < $n_replicas} {incr i} {
append input "$f.$i "
}
colvars on
cv config "
(...)
abf {
inputPrefix $input
(...)"
Alternately, for the Zheng/Yang estimator, see the -mergemwabf option in
the documentation. To do that, remember that you need to enable the
Zheng/Yang estimator when running all the calculations!
Best,
Jerome
On 26 April 2017 at 13:17, Souvik Sinha <souvik.sinha893_at_gmail.com> wrote:
> Sorry, I got most of my answers in http://www.ks.uiuc.edu/Rese
> arch/vmd/current/ug/node235.html
>
> Still, doubt remain regarding applicability of Multiple-walker strategy.
> And, are these '.zgrad' & '.czar.grad' are different?
>
> On Wed, Apr 26, 2017 at 12:10 PM, Souvik Sinha <souvik.sinha893_at_gmail.com>
> wrote:
>
>> Hi,
>> I was trying eABF (on 1D) with the example system given within NAMD 2.12
>> package. It seems to be generating pmf files directly along with '.grad' &
>> '.count' without any post-processing script. Maybe that's the whole point
>> of "on-the-fly" implementation of eABF. But there are 2 files for
>> pmf/grad/count. Along with normal '(abf).grad/.pmf', there are
>> '(abf.czar).pmf/.grad'. And along with normal '.count', there is a
>> '.zcout'. I believe these normal .grad/.pmf is the output of Zhang-Yang
>> estimator & .czar.* is of CZAR estimator. Am I right? And what's this
>> .zcount ?
>>
>>
>>
>> Then I tried 2D with the NANMA system (provided with ABF tutorial files).
>> Now, whenever I am trying to merge '.grad' & '.count' of individual
>> windows using 'colvar-merge.in' , its giving the following error:
>>
>> " colvars: Error opening eABF z-gradient file output/colvarBo.zgrad for
>> reading "
>>
>> There aren't any '.zgrad' file generated as an output of any eABF run.
>> Again only '.czar.grad' files are there. If these '.zgrad' & '.czar.grad'
>> are same then I can rename & proceed further. But I am not certain. Please
>> enlighten me.
>>
>>
>>
>> And finally, is multiple-walker algorithm applicable for 2D using eABF?
>>
>> Looking for useful suggestions. Thanks.
>>
>> --
>> 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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