From: Tugba Nogay (gntuba_at_yahoo.com)
Date: Fri Jan 06 2012 - 10:53:36 CST
Hello,
I am trying to set up ABF simulations to get PMF of ion translocation through a membrane channel. My inputs are copied below. I noticed (through visual inspection, also wrote out pdb files for atom index 96913) that the ion that the forces are applied to moves out of the range even though I specify 100 kcal/mol-A force constant to upper and lower wall (I also tried 1000). There may be an apparent mistake that I can't see. I would appreciate it if someone can point out where the problem is.
Configuration file:
margin 2.5
# protocol params
firsttimestep 0
# initial config
coordinates window5.pdb
temperature 323.15
#velocities efw12.vel
seed 13579
#extendedSystem mid1.xsc
# output params
outputname mid1
binaryoutput no
restartname mid1
restartfreq 10000
DCDfile mid1
DCDfreq 2000
DCDUnitcell yes
outputEnergies 2000
outputPressure 2000
colvars on
colvarsConfig mrestrain2.in
#outputSystemForce 1000
#outputAppliedForce 1000
# integrator params
timestep 0.5;
nonbondedFreq 1;
fullElectFrequency 1;
# force field params
structure ../step5_assembly.xplor.psf
paraTypeCharmm on
parameters ../toppar/namd/par_all22_prot.prm;
parameters ../toppar/namd/par_all27_na.prm;
parameters ../toppar/namd/par_allxx_sugar.inp;
parameters ../toppar/namd/par_all36_lipid.prm;
parameters ../toppar/namd/par_all36_cgenff.prm;
parameters ../toppar/namd/toppar_water_ions.str;
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 14.0
pairlistdist 16.0
stepspercycle 20
# periodic boundary conditions
cellBasisVector1 108.879 0.0 0.0
cellBasisVector2 54.4395 94.0703 0.0
cellBasisVector3 0.0 0.0 97.992
cellOrigin 0.0 0.0 1.0395;
XSTfile middlex
XSTfreq 2000
wrapWater on
wrapAll on
wrapNearest on
# PME
PME on
#PMEGridSpacing 1.0
PMEInterpOrder 6;
PMEGridSizeX 148
PMEGridSizeY 148
PMEGridSizeZ 96
# Dynamics
rigidBonds water
useGroupPressure yes;
useFlexibleCell yes;
useConstantRatio yes;
langevin on;
langevinPiston on;
langevinPistonTarget 1.01325;
langevinPistonPeriod 100.0;
langevinPistonDecay 50.0;
langevinPistonTemp 323.15;
langevinTemp 323.15
langevinDamping 1
langevinHydrogen off
# Execution script
run 100000
Colvars input:
colvarsTrajFrequency 1000
colvarsRestartFrequency 1000
colvar {
name Translocation
width 0.1
lowerboundary -6.00
upperboundary 0.0
lowerwallconstant 100.0
upperwallconstant 100.0
distanceZ {
main {
atomnumbers { 96914 }
}
ref {
atomnumbers {
5 822 1579 2391 3165 3942 4737 5513 6297 7082 7857 8631 9441 10225
29 841 1603 2410 3177 3953 4756 5524 6308 7097 7873 8651 9452 10239 ...... ---> CA atoms of the protein
}
}
axis ( 0.0, 0.0, 1.0 )
}
}
abf {
colvars Translocation
fullSamples 1000
}
>From window5.pdb:
ATOM 96912 SOD SOD S 10 -51.392 30.755 -44.335 0.00 0.00 SOD
ATOM 96913 SOD SOD S 11 -19.337 27.654 42.819 0.00 0.00 SOD
ATOM 96914 SOD SOD S 12 7.290 7.262 -5.057 1.00 0.00 SOD
ATOM 96915 SOD SOD S 13 -11.144 5.802 -31.093 0.00 0.00 SOD
ATOM 96916 SOD SOD S 14 8.680 16.387 42.718 0.00 0.00 SOD
Thanks,
TNogay
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