From: amit banerjee (amit_informatics_at_yahoo.com)
Date: Wed Jul 13 2011 - 03:03:45 CDT
Dear Friends,
I need a small help from you guys, presently I am running a NAMD simulation in picoscale using the more or less default protocol as attached with this mail and provided below. Kindly let me know what are the changes i should make in this .conf file to obtain a nanoscale simulation?
My other question is what is the range of the cut off values can be used in the protocol for to perform a successful nanoscale simulation for a protein ranging from 250-500 amino acid in general.
Picoscale .conf file applied:
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ../common/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
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Spherical boundary conditions
sphericalBC off
sphericalBCcenter -1.42082428932 3.25120377541 2.19151377678
sphericalBCr1 26.0
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100000
reinitvels $temperature
run 250000 ;# 50ps
Waiting for reply.
Best Regards,
Amit Kumar Banerjee
IICT
Hyderabad
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