From: dora guzman (dguzman_at_uci.edu)
Date: Wed Feb 08 2006 - 17:05:51 CST
attached mail follows:
Hello,
I'm having a problem minimizing and equilibrating my protein. It's fully
solvated (total of 28,000 atoms). RMSD analysis after ~1.5 ns shows that
the protein is reaching a plateau, however, as the equilibrating
continues after a total of 2 ns the RMSD begins increasing from
approximately 1.5 Angstroms to almost 3 Angstroms! I'm not sure what's
going on. I've used the same parameters, PME grid sizes, etc. when
restarting the run. How long does it usually take for a protein to reach
equilibration? I'm attaching a restart configuration file.
Any input is greatly appreciated.
-dg
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Protein 1S12 in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../commonS12/s12_ION.psf
coordinates ../commonS12/s12_ION.pdb
# continuing a run
bincoordinates ../commonS12/s12_ION_eq5-1.restart.coor.old
binvelocities ../commonS12/s12_ION_eq5-1.restart.vel.old
extendedsystem ../commonS12/s12_ION_eq5-1.restart.xsc.old
set outputname s12_ION_eq5-2
firsttimestep 544500
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../commonS12/par_all22_prot.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds none ;# all needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 79. 0. 0.
cellBasisVector2 0. 74. 0.
cellBasisVector3 0. 0. 73.
cellOrigin 34.5299 26.1145 29.7084
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 81
PMEGridSizeY 81
PMEGridSizeZ 81
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp 300
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {0} {
fixedAtoms on
fixedAtomsFile ../commonS12/s12_fixedprot_eq.ref
fixedAtomsCol B
}
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 1000
reinitvels 300
run 1144500 ;# 600 ps
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