From: mgssal (mgssal_at_gmail.com)
Date: Sun Jul 12 2009 - 03:22:46 CDT
Hello,
I am trying to minimize my protein in a water box. The minimization
run seems to run fine, with no errors in the log file; however one of
the residues (#153) seems to be off the rest of the protein at the end
of the run.
ATOM 136 CA ASN U 152 -9.909 112.197 81.551 1.00 0.00 U
ATOM 137 CA ILE U 153 -8.986 113.903 -23.813 1.00 0.00 U
ATOM 138 CA GLN U 154 -11.491 114.281 77.206 1.00 0.00 U
The end of the log file is as follows:
ENERGY: 10000 19574.8004 14130.9889 2429.1344
62.6588 -639534.6359 75778.8480 0.0000
0.0000 0.0000 -527558.2054 0.0000
-527558.2054 -527558.2054 0.0000 -4169.0182
-4165.5559 1383393.0000 -4169.0182 -4165.5559
WRITING COORDINATES TO DCD FILE AT STEP 10000
WRITING COORDINATES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 10000
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 10000 TO 310 KELVIN.
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 10000
WRITING COORDINATES TO OUTPUT FILE AT STEP 10000
CLOSING COORDINATE DCD FILE
WRITING VELOCITIES TO OUTPUT FILE AT STEP 10000
==========================================
WallClock: 83540.904668 CPUTime: 78086.737012 Memory: 425660 kB
Program finished.
My conf file pretty much follows the one in the tutorial. Below it
is appended for completeness.
Thanks,
--mgssal
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./amu_wb.psf
coordinates ./amu_wb.pdb
set temperature 310
set outputname amu_wb_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ./par_all27_prot_lipid.inp
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds 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 $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 111. 0. 0.
cellBasisVector2 0. 121. 0.
cellBasisVector3 0. 0 103.
cellOrigin 11. 119. 56
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 108
#PMEGridSpacing 1.0
# 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 $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 10000
reinitvels $temperature
#run 2500 ;# 5ps
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