From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Fri May 26 2017 - 00:45:37 CDT
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
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:19 CST