From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Mon Mar 04 2013 - 05:55:07 CST
Hi,
I am running a DMPC simulation since yesterday, and it says, "TIMING:
47500 CPU: 39142.3, 0.699396/step Wall: 39142.3, 0.699396/step,
39.5353 hours remaining, 57.136719 MB of memory in use."
I used the following comands to create a pdb file for fixed atoms:
set all [atomselect top all]
set fix [atomselect top "protein and name N"]
set fix [atomselect top protein and backbone]
after that, you have to type the following:
$all set beta 0
$fix set beta 1
$all writepdb dmpcf.pdb
And this is the conf file:
In the program is was recommended that I run minimization 250, 000
steps. Is this the reason the simulation is so long?
Thank you,
Mihaela
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../DMPC/dmpc_autopsf.psf
coordinates ../DMPC/dmpc.pdb
outputName dmpcout
set temperature 300
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all36_lipid.prm
parameters par_all27_prot_lipid.inp
# NOTE: Do not set the initial velocity temperature if you
# have also specified a .vel restart file!
temperature $temperature
# Periodic Boundary Conditions
# NOTE: Do not set the periodic cell basis if you have also
# specified an .xsc restart file!
if {1} {
cellBasisVector1 46.2735 0. 0.
cellBasisVector2 0. 46.2735 0.
cellBasisVector3 0. 0. 62.3748
cellOrigin 0. 0. 0.
}
wrapWater on
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
vdwForceSwitching on
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
#PME (for full-system periodic electrostatics)
if {1} {
PME yes
PMEGridSizeX 50
PMEGridSizeY 50
PMEGridSizeZ 65
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
restartfreq 1000 ;# 1000steps = every 2ps
dcdfreq 1000
xstFreq 1000
outputEnergies 50
outputPressure 50
# Fixed Atoms Constraint (set PDB beta-column to 1)
if {1} {
fixedAtoms on
fixedAtomsFile dmpcf.pdb
fixedAtomsCol B
fixedAtomsForces on
}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
if {1} {
minimize 1000
reinitvels $temperature
}
run 250000 ;# 0.5 ns
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