**From:** Souvik Sinha (*souvik.sinha893_at_gmail.com*)

**Date:** Fri May 26 2017 - 10:53:04 CDT

**Next message:**Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]: "RE: Error regarding missing angles between perturbed groups for fep calculation"**Previous message:**Jérôme Hénin: "Re: Querries on eABF"**In reply to:**Jérôme Hénin: "Re: Querries on eABF"**Next in thread:**Souvik Sinha: "Re: Querries on eABF"**Reply:**Souvik Sinha: "Re: Querries on eABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

**Next message:**Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]: "RE: Error regarding missing angles between perturbed groups for fep calculation"**Previous message:**Jérôme Hénin: "Re: Querries on eABF"**In reply to:**Jérôme Hénin: "Re: Querries on eABF"**Next in thread:**Souvik Sinha: "Re: Querries on eABF"**Reply:**Souvik Sinha: "Re: Querries on eABF"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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