Re: Querries on eABF

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Fri May 26 2017 - 10:53:04 CDT

Ok thanks. I get it now.

On Fri, May 26, 2017 at 9:00 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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
>>
>
>

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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