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 ¦Â-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
**************************************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:06 CST