From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Wed Jul 13 2011 - 10:48:48 CDT
Hi,
I have asked this question previously also . I have repeated the
equilibration again , but still the protein moves out of the box.
here is the configuration file that I used for minimization and npt
equilibration :-
Minimization
===========
numsteps 100000
minimization on
dielectric 1.0
coordinates ./ionized.pdb
outputname complex_min
outputEnergies 1000
binaryoutput no
DCDFreq 1000
restartFreq 1000
structure ./ionized.psf
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 8.0
cutoff 12.0
pairlistdist 13.5
margin 0.0
stepspercycle 10
===============================
npt equilibration
------------------------
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
#GFP in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ./ionized.psf
coordinates ./ionized.pdb
set temperature 310
set outputname complex_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
binCoordinates ./complex_min.restart.coor
binaryrestart yes
extendedSystem ./complex_min.restart.xsc
paraTypeCharmm on
parameters ../common/par_all27_prot_na.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
margin 2.5
# 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 65. 0. 0.
cellBasisVector2 0. 53. 0.
cellBasisVector3 0. 0 49.
cellOrigin 0. 0. 0.
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 60
PMEGridSizeY 60
PMEGridSizeZ 60
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
#Note the lack of langevinpiston, which is the pressure control
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
numsteps 30000
I tried using pbc wrap by using the command pbc wrap -centersel protein but
whole of the box and protein comes out in the form of lines...
Pls help as I am not able to move on with my experiment
-- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46010_at_yahoo.com
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