From: Danilo Di Maio (danilo.dimaio_at_gmail.com)
Date: Tue Apr 14 2015 - 05:41:24 CDT
Dear NAMD community,
I am studying the free energy profile for the translocation of an ion inside a protein channel, using the ABF method implemented in NAMD 2.9. I divided my reaction coordinate (distance along the z-axis) in several windows (5 Angstrom each) taking as reference point the center of mass of a stretch of residues inside the protein channel.
Surprisingly, i ran into a very strange problem. All the simulations terminated successfully but I noted that for some windows, NAMD was able to produce normal .grad and .count output files (i.e. filled with values), while for other windows the .grad and .count files were completely filled with zeros in each bin. This looked very strange to me since all the input files were substantially equal (i simply duplicated several times the first one and changed only those options regarding input .coor .vel .xsc files and the boundaries of the investigated region in the colvar file). I payed attention that all the simulation options were equal among the various simulations.
When I visually inspected the various trajectories, i noted that in the windows for which NAMD could produce "correct" .grad and .count output files the ion is able to move along the z-axis, while in the windows for which NAMD produced .count and .grad files filed with zeros the ion is like "constrained" to move on the XY plane only.
Though, on one hand, this maybe explains why in some windows gradients and counts are everywhere zero (the ion doesn't explore regions along the z-axis), on the other hand i have really no idea about how to fix this issue, because apparently this problem is not related to differences in the input files. As a countercheck i compared the log files of the various simulations and they also looked very similar.
Moreover i tried to use different versions of NAMD (2.9 and 2.9b3) obtaining the same outcome.
Below i attach a NAMD input file and a colvar file used in the simulation, marking as bold those options which were different among the various windows.
I would really appreciate if you could help me to solve this issue please.
Thanks in advance
Danilo
abf.conf
set inputname equi
set outputname 14th_win
set restart name 14th_win_restart
paraTypeCharmm on
parameters par_all27_prot_lipidNBFIX.prm
parameters par_all36_lipid.prm
structure Ca2+_PMF_autopsf.psf
coordinates Ca2+_win14_autopsf.pdb
bincoordinates $inputname.coor
exclude scaled1-4
1-4scaling 0.833333
outputname $outputname
binaryoutput yes
binaryrestart yes
XSTfile $outputname.xst;
XSTfreq 500;
restartfreq 500
outputEnergies 500
outputTiming 500
outputMomenta 500
outputPressure 500
dcdfreq 10000 ;
DCDfile $outputname.dcd
timestep 2
firsttimestep 0
cutoff 10
switching on
switchdist 8
pairlistdist 14
stepspercycle 10
margin 0
rigidBonds all
rigidIterations 300
rigidTolerance 0.00001
symmetryRestraints on
symmetryFile 5-fold-symmetry.pdb
symmetrykFile FK_file.pdb
binvelocities $inputname.vel
PME yes;
PMEInterpOrder 4
PMEGridSpacing 1.0
extendedSystem $inputname.xsc
wrapall on
wrapWater off
wrapNearest off
fullElectFrequency 2
nonbondedFreq 1
langevin on
langevinDamping 5
langevinTemp 310
langevinHydrogen off
useGroupPressure yes
useFlexibleCell yes
useConstantRatio yes
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310
colvars on
colvarsConfig abf14.in
run 2500000
abf14.in
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
name Na+_XY_restraint
width 0.5
lowerboundary 15.0
upperboundary 75.0
lowerwallconstant 10.0
upperwallconstant 10.0
distanceXY {
main {
atomnumbers { 398004 398005 398006 398007 398008 398009 398010 398011 398012 398013 398014 398015 398016 398017 398018 398019 398020 398021}
}
ref {
atomnumbers { 4239 9655 15071 20487 25903 }
}
axis ( 1.0, 1.0, 0.0 )
}
}
colvar {
name Translocation
width 0.1
lowerboundary -7.5
upperboundary -2.5
lowerwallconstant 50.0
upperwallconstant 50.0
distanceZ {
main {
atomnumbers { 398022 }
}
ref {
atomnumbers { 4239 9655 15071 20487 25903 }
}
axis ( 0.0, 0.0, 1.0 )
}
}
colvar {
name XY_restraint
width 0.5
lowerboundary 0.0
upperboundary 15.0
lowerwallconstant 100.0
upperwallconstant 100.0
distanceXY {
main {
atomnumbers { 398022 }
}
ref {
atomnumbers { 4239 9655 15071 20487 25903 }
}
axis ( 1.0, 1.0, 0.0 )
}
}
abf {
colvars Translocation
fullSamples 800
historyFreq 250
}
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