From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Thu May 25 2017 - 05:02:32 CDT
While running MW_eabf, I am actually getting 4 sets " grad " files for each
replica [ e.g. colvar2.1.grad, colvar2.1.zgrad, colvar2.1.czar.grad
& colvar2.eabf.1.grad ] & 3 sets of " count " files [colvar2.1.count,
colvar2.1.zcount & colvar2.eabf.1.count]. There are significant difference
in the values of those files.
I understand that " *.zcount " is the z-histogram & " *.zgrad " contains
z-averaged restraints forces. But, what is need of the other sets ? I
guess, one of them is related to Z-Y estimator but which one is it ?
I found " *outputName*.czar.grad: current estimate of the free energy
gradient (grid), in multicolumn ". Then where this file is differing from
outputName.[ReplicaID].grad & outputName.eabf.[ReplicaID].grad ?
Part of the configuration file (related to input-output) is here :
set outName colvar2
structure vacuum.psf
parameters common/par_all22_prot.inp
paraTypeCharmm on
coordinates equilvac.coor
velocities equilvac.vel
outputname $outName.[myReplica]
restartname $outName.[myReplica]
*****
***
source ../eabf.tcl
set eabf_inputname 0 ;# restart file name or
"0"
set eabf_outputname colvar2.eabf.[myReplica] ;# restart file name
set eabf_temperature 300
set eabf_outputfreq 10000
**************************
*****************
# ABF
colvars on
colvarsConfig colvars2.in
##### Replica Exchange ####################
source /apps/NAMD_2.12_Linux-x86_64-multicore/lib/selectionRules.tcl
source /apps/NAMD_2.12_Linux-x86_64-multicore/lib/resampleWalkers.tcl
source /apps/NAMD_2.12_Linux-x86_64-multicore/lib/minExchanges.tcl
firsttimestep 0
replicaUniformPatchGrids on
set m 1000
set sharedFreq 10000
for {set i 0} {$i < $m} {incr i} {
run $sharedFreq
cv bias abf1 share
}
*************************************************************
Please help me out.
Thank you.
On Fri, Apr 28, 2017 at 10:57 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
wrote:
> Thanks for the reply.
>
> On Fri, Apr 28, 2017 at 2:30 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> Hi Souvik,
>>
>> Indeed, you can always find the current documentation here:
>> http://colvars.github.io/
>>
>> Multiple-walker eABF works fine. To estimate the free energy, you can
>> merge CZAR results from different walkers. For that, run a single eABF
>> simulation for zero steps, providing the output from all walkers as
>> inputPrefix
>> <http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-590006.1.2>.
>> To get all the necessary input, you need to enable writeCZARwindowFile
>> <http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#x1-640006.2.1> during
>> your calculations (if you forgot, you can also extract this information
>> from state files, but that will an extra step).
>>
>> The NAMD config for combining might look like this, using Tcl to build
>> the list of files:
>>
>> set f base_name
>> set n_replicas 42
>> set input ""
>>
>> for {set i 0} {$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--94eb2c05b67cc1134805505651d3--
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