From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 26 2017 - 10:30:46 CDT
Hi Souvik,
The .count/.grad/.pmf files are the ABF results for the extended
coordinate. They can be useful to monitor the progress of the simulation,
but you don't need to worry about them.
*.eabf.* files are related to the Z/Y estimator. *.czar.* are related to
the CZAR estimator. They should converge to just about the same values.
Jerome
On 26 May 2017 at 00:45, Souvik Sinha <souvik.sinha893_at_gmail.com> wrote:
> Thanks for the reply.
>
> I know that each replica would separately give output of its grad & counts
> (classical ABF). But here in eABF, each replica is giving multiple grads &
> count files as I mentioned in the previous mail. One set is for CZAR
> estimator that I understood but what about other sets? how do I suppose to
> handle them?
>
> On Fri, May 26, 2017 at 2:36 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>
>> Hi,
>>
>> Each replica produces its own gradient, count, and PMF files, which are
>> synchronized every shareFreq steps. For usual values of shareFreq, these
>> files should be very similar. How different they are depends on shareFreq,
>> which is the number of steps between synchronization of the replicas. If I
>> remember correctly, output of the .grad, .count, etc. files happens before
>> synchronization, so if shareFreq and colvarsRestartFrequency are the same,
>> your files will be different by shareFreq samples.
>>
>> 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 Thu, May 25, 2017 at 5:02 AM, Souvik Sinha <souvik.sinha893_at_gmail.com>
>> wrote:
>>
>>> 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
>>>
>>
>>
>
>
> --
> Souvik Sinha
> Research Fellow
> Bioinformatics Centre (SGD LAB)
> Bose Institute
>
> Contact: 033 25693275
>
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