From: Maria Pikoula (maria.pikoula_at_eng.ox.ac.uk)
Date: Fri May 04 2012 - 16:46:03 CDT
Dear all
I have been using the TclBC scripting function to impose a force in my system in order to implement flow. It is applied to the water oxygens in every time step. I would like for this force to be applied less frequently as it slows down the computation speed considerably. When I try to apply the force every 100 steps I get this error message on the first go:
FATAL ERROR: tclBCScript failed to call nextatom until failure
if I simply apply the force every time step, the simulation is fine.
Thank you for any help, comments.
Maria
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Here I copy the configuration file and tcl script:
Configuration file:
coordinates flow_fast_rextra2.coor
numsteps 55000000
set temp 300
set outputname flow_fast_plus110
binaryoutput no
binaryrestart no
firsttimestep 0
velocities flow_fast_rextra2.vel
# Input
paraTypeCharmm off
amber on
parmfile man_WAT.top
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching off
pairlistdist 13.5
# Integrator Parameters
timestep 2
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control Using Berendsen Method (Coupling)
tCouple on
tCoupleTemp $temp
tCoupleFile temp_coupling.pdb
tCoupleCol B
wrapAll off
extendedSystem flow_fast_rextra2.xsc
# PME (for full-system periodic electrostatics)
PME yes
#PMEGridSizeX 100
#PMEGridSizeY 100
#PMEGridSizeZ 100
PMEGridSpacing 1.0
# Constant Pressure Control (variable volume)
useGroupPressure yes
useFlexibleCell no
useConstantArea no
BerendsenPressure on
BerendsenPressureTarget 1.01325 ;# in bar -> 1 atm
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 100
BerendsenPressureFreq 10
# Output
outputName $outputname
velDCDfile flow_fast_plus110_vel.dcd
velDCDfreq 200
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 200
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
constraints on
consref constrained_atoms.pdb
conskfile constrained_atoms.pdb
conskcol B
tclBC on
tclBCScript {
set zLo -9. ;# lower plane where forces are applied
set zHi 9. ;# top plane where forces are applied
set dz 3. ;# half-width of the layer
set TOL 6. ;# drop atoms that far from either layer
set start 232
set end 18628
set force 0.00001
set pdbSource man_WAT.pdb
set tclBCScript flow.tcl
source $tclBCScript
}
tclBCArgs { }
Tcl Script:
set atomList {} ;
for { set i $start } { $i<=$end } { incr i 3 } { lappend atomList $i; }
puts "[llength $atomList] water oxigens atoms found"
proc calcforces {step unique} {
global atomList force;
if {$step % 100 == 0} {
while {[nextatom]} {
if { [lsearch $atomList [getid]] == -1 } {continue; }
addforce "[expr {$force}] 0.0 0.0";
}
}
}
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