Re: Restart multiple walker ABF

From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Mon May 23 2016 - 01:13:10 CDT

The previous reply somehow omits the following lines.

The 'colvar.traj' files I am getting from the multiple walker simulations
have lines with repeated step numbers although the values of the colvar are
different.
For example '*abf-22-p2-replica.0.colvars.traj'* contains the follwing
lines -

# step Translocation fs_Translocation fa_Translocation
      280000 3.37579040918854e-02 0.00000000000000e+00
 3.94250103934920e-01
      281000 3.04982765963392e-01 -3.80475221653587e+01
-3.23602212565702e+00
      281000 3.04982765963392e-01 -3.57517245109738e+01
-3.12575708458790e+00
      282000 2.86269116808262e-01 5.17905626287114e+01
-3.51115402547890e+00
      282000 2.86269116808262e-01 3.96288633143963e+01
-3.51266503703765e+00
      283000 3.37453024702899e-01 6.44092188309401e+01
-2.73833420465494e+00
      283000 3.37453024702899e-01 6.92727441837536e+01
-2.76445168941741e+00
      284000 5.29770158955818e-01 -8.58429320121528e+01
-1.68959558429508e+00
      284000 5.29770158955818e-01 -8.66894122805514e+01
-1.67863316704566e+00

Is this incorrect ?

Thank you in advance.

Atanu Maity
Bioinformatics Center
Bose Institute

On Mon, May 23, 2016 at 10:25 AM, Atanu Maity <atanuchem48_at_gmail.com> wrote:

> Thank you sir, it works, sorry for the late reply.
>
> I have another query which may seem to be a cross-post. I am sorry for
> that.
> The 'colvar.traj' files I am getting from the multiple walker simulations
> have lines with repeated step numbers although the values of the colvar are
> different.
>
> For example '*abf-22-p2-replica.0.colvars.traj'* contains the follwing
> lines -
>
> # step Translocation fs_Translocation fa_Translocation
> 280000 3.37579040918854e-02 0.00000000000000e+00
> 3.94250103934920e-01
> 281000 3.04982765963392e-01 -3.80475221653587e+01
> -3.23602212565702e+00
> 281000 3.04982765963392e-01 -3.57517245109738e+01
> -3.12575708458790e+00
> 282000 2.86269116808262e-01 5.17905626287114e+01
> -3.51115402547890e+00
> 282000 2.86269116808262e-01 3.96288633143963e+01
> -3.51266503703765e+00
> 283000 3.37453024702899e-01 6.44092188309401e+01
> -2.73833420465494e+00
> 283000 3.37453024702899e-01 6.92727441837536e+01
> -2.76445168941741e+00
> 284000 5.29770158955818e-01 -8.58429320121528e+01
> -1.68959558429508e+00
> 284000 5.29770158955818e-01 -8.66894122805514e+01
> -1.67863316704566e+00
>
>
> Is this incorrect ?
>
> Thank you in advance.
>
> Atanu Maity
> Bioinformatics Centre
> Bose Institute
>
>
> On Fri, May 20, 2016 at 2:28 AM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
>
>> You have 4 replicas that write four different restart files indexed by
>> [myReplica]. When you restart, each system should restart from its restart
>> file:
>> binCoordinates $inputname.[myReplica].coor
>> binVelocities $inputname.[myReplica].vel
>> extendedSystem $inputname.[myReplica].xsc
>>
>> 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 19, 2016 at 3:32 AM, Atanu Maity <atanuchem48_at_gmail.com>
>> wrote:
>>
>>> Dear users,
>>>
>>> I am facing this problem while trying to restart an REMD (multiple
>>> walker) run as a part of ABF simulation. I start the simulation using the
>>> following command line –
>>>
>>>
>>> mpirun -np 32 namd2 +replicas 4 abf-replica.namd +stdout
>>> replica4/%d/job4.%d.log &
>>>
>>>
>>> Four replicas were running using 8 core each properly.
>>>
>>>
>>> The input contains the following lines –
>>>
>>>
>>>
>>> structure step5_assembly.xplor_ext.psf
>>>
>>> coordinates step5_assembly.pdb
>>>
>>> set temp 303.15;
>>>
>>> set outputname replica4/abf-22-prod2.[myReplica]
>>>
>>> set inputname abf-22-prod1.1
>>>
>>> binCoordinates $inputname.coor
>>>
>>> binVelocities $inputname.vel
>>>
>>> extendedSystem $inputname.xsc
>>>
>>> outputname $outputname
>>>
>>> restartfreq 10000;
>>>
>>> dcdfreq 2000;
>>>
>>> dcdUnitCell yes;
>>>
>>> xstFreq 10000;
>>>
>>> outputEnergies 10000;
>>>
>>> outputTiming 10000;
>>>
>>>
>>> # Force-Field Parameters
>>>
>>> paraTypeCharmm on;
>>>
>>> parameters toppar-namd/par_all36_prot.prm;
>>>
>>> parameters toppar-namd/par_all36_lipid.prm;
>>>
>>> parameters toppar-namd/toppar_all36_lipid_cholesterol.str;
>>>
>>> parameters toppar-namd/toppar_all36_lipid_glycolipid.str;
>>>
>>> parameters toppar-namd/toppar_all36_lipid_bacterial.str;
>>>
>>> # These are specified by CHARMM
>>>
>>> exclude scaled1-4
>>>
>>> langevinPistonTemp $temp;
>>>
>>>
>>>
>>> # Constant Temperature Control
>>>
>>> langevin on; # langevin dynamics
>>>
>>> langevinDamping 1.0; # damping coefficient of 1/ps
>>> (keep low)
>>>
>>> langevinTemp $temp; # random noise at this level
>>>
>>> langevinHydrogen off; # don't couple bath to hydrogens
>>>
>>>
>>>
>>> colvars on
>>>
>>> colvarsConfig abf-22-bb-replica.in
>>>
>>> ## Replica Exchange ##
>>>
>>> ##SElectionRules will be applied at each 100 steps###
>>>
>>> source /apps/NAMD_2.11b1_Source/lib/selectionRules.tcl
>>>
>>> source /apps/NAMD_2.11b1_Source/lib/resampleWalkers.tcl
>>>
>>> source /apps/NAMD_2.11b1_Source/lib/minExchanges.tcl
>>>
>>> firsttimestep 230000
>>>
>>> replicaUniformPatchGrids on
>>>
>>> set n 12500
>>>
>>> set sharedFreq 100
>>>
>>> for {set i 0} {$i < $n} {incr i} {
>>>
>>> run $sharedFreq
>>>
>>> cv bias abf1 share
>>>
>>> if {$i % 50 == 49} {
>>>
>>> selectionRules
>>>
>>> }
>>>
>>> }
>>>
>>>
>>>
>>> The problem with the restart is that I did not understand which restart
>>> files (.coor, .vel, .state) should I use because I have four sets of such
>>> files.
>>>
>>
>>
>

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