ABF simulation

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

 

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:38 CST