From: Atanu Maity (atanuchem48_at_gmail.com)
Date: Thu May 19 2016 - 03:36:30 CDT
Sorry, I forget to mention.
Thanks in advance.
Regards,
Atanu Maity
Research Scholar
Bose Institute
On Thu, May 19, 2016 at 2:02 PM, 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.
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:26 CST