From: Subbarao Kanchi (ksubbu85_at_gmail.com)
Date: Wed Sep 17 2014 - 12:04:44 CDT
Dear all,
1) I am trying to run implicit solvent lipid bilayer
simulation.I have use the fallowing namd configuration file to lipid
bilayer simulation with GBIS but it collapsing (lipids are coming out of
the bilayer) the lipid bilayer structure. Is any one know or experienced
this problem.
2) Is the distance dependent dielectric method implemented in
the NAMD. If yes, how to use it.
I checked the mailing list and user guide but there is no use in
this contest. I will appreciate any suggestions in this regards.
namd configure file:
structure not_water.psf
coordinates not_water.pdb
outputName eq_nvt_5ns
set temperature 0
set temperature1 303.15
set cons 0
# Input
paraTypeCharmm on
parameters par_all36_lipid.prm
parameters test_petim.prm
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature1
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 136.475 0. 0.
cellBasisVector2 0. 135.475 0.
cellBasisVector3 0. 0. 200.0
cellOrigin 0.0 0.0 0.0
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
GBIS on
cutoff 16.0
switching on
switchdist 15.0
pairlistdist 18.0
# Integrator Parameters
timestep 2.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {0} {
PME yes
PMEGridSpacing 1.0
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature1
restartfreq 1000 ;# 1000steps = every 1ps
dcdfreq 1000
xstFreq 1000
outputEnergies 1000
outputPressure 1000
run 2500000 ;# 5.0 ns
Regards,
Subbu.
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