ABF:problems with calculating Free Energy Profile

From: supram_at_nankai.edu.cn
Date: Sun Nov 16 2008 - 20:55:39 CST

dear everyone,
I am running a free energy calculation with ABF method for the complex of -CD
with L-glutamic acid (Glu). The abf coordinate is zCoord.Prior to the ABF run,I
have made a NPT simulition for 2ns with the abf abf1 { 14 35 56 77 98 119 140 }and
abf abf2 { 149 150 164 165 } atoms are fixed. When running the free energy
calculation, the the abf abf1 { 14 35 56 77 98 119 140 }atoms are still fixed and
the abf abf2 { 149 150 164 165 } atoms are constrainted on the XY plan to make
sure the L-glutamic acid (Glu)moving on the Z axis. The calculated Free Energy
Profile is abnormaly increased, and the running time for the calculation is only
2ns,whith is very short!

I want to know the reasons for the problems, I will very be deeply grateful for
your help, thank you very much!
Here are my config file for the MD and ABF simulation file.
MD simulation config file:
*******************************************************************************
structure bcdlglu_wb_na.psf
coordinates bcdlglu_wb_na.pdb

paraTypeCharmm on
parameters par_all22_prot.inp
parameters CSFF_parm.inp
temperature 298.15

exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 12.0
pairlistdist 16.0

timestep 2.0
rigidbonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

langevin on
langevinDamping 1
langevinTemp 298.15
langevinHydrogen on

useGroupPressure yes
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 298.15

cellBasisVector1 35.4259986877 0. 0.
cellBasisVector2 0. 35.3390007019 0.
cellBasisVector3 0. 0. 58.4050006867
cellOrigin -0.139399647713 0.539306521416 4.29369020462

wrapwater on
wrapall on

PME on
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 60

fixedatoms on
fixedatomsfile bcdlglu_wb_na_f.pdb
fixedatomscol B

outputName output-MD
binaryoutput no
outputEnergies 1000
outputTiming 1000
outputPressure 1000
dcdfile bcdlglu_wb.dcd
dcdfreq 1000
dcdunitcell yes
xstfreq 1000
restartname restart
binaryrestart no
restartfreq 1000

minimize 10000

run 1000000
******************************************************************************
ABF simulation config file:
****************************************************************************
structure bcdlglu_wb_na.psf
coordinates restart.coor
velocities restart.vel
extendedsystem restart.xsc
firsttimestep 1010000

paraTypeCharmm on
parameters par_all22_prot.inp
parameters CSFF_parm.inp

exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 12.0
pairlistdist 16.0

timestep 1.0
rigidbonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

langevin on
langevinDamping 1
langevinTemp 298.15
langevinHydrogen on

useGroupPressure yes
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1
langevinPistonPeriod 100
langevinPistonDecay 50
langevinPistonTemp 298.15

wrapwater on
wrapall on

PME on
PMEGridSizeX 36
PMEGridSizeY 36
PMEGridSizeZ 60

fixedatoms on
fixedatomsfile bcdlglu_wb_na_f.pdb
fixedatomscol B

constraints on
consref restart.coor
conskfile bcdlglu_wb_na_h.pdb
conskcol B
selectconstraints on
selectconstrx on
selectconstry on
selectconstrz off

outputName output-ABF
binaryoutput no
outputEnergies 1000
outputTiming 1000
outputPressure 1000
dcdfile bcdlglu_wb.dcd
dcdfreq 1000
dcdunitcell yes
xstfreq 1000
restartname restart-1
binaryrestart no
restartfreq 1000

source /nfs/s09r2p2/yuliu_nk/NAMD2.6-1/Abf/abf.tcl

abf coordinate zCoord

abf abf1 { 14 35 56 77 98 119 140 }

abf abf2 { 149 150 164 165 }

abf ximin -12

abf ximax 12

abf dxi 0.1

abf fullsamples 1000

abf dsmooth 0.1

abf forceconst 40

abf applybias yes

abf outputfreq 1000

abf writexifreq 1000

abf outfile bcdlglu.abf

run 12000000
**************************************************************************


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