Two questions about free dynamics simulation

From: wayj86 wayj86 (wayj86_at_gmail.com)
Date: Fri Oct 31 2008 - 21:46:25 CDT

Hi all,

I want to ask you two questions about FMD.

1.I feel the FMD is somwhat like equilibration but do not control the
temperature and pressure. So please correct me if the configuaration file is
wrong.

structure ionized.psf
# coordinates ionized.pdb
outputName free

set temperature 310

# Continuing a job from the restart files
if {1} {
set inputname eq
coordinates $inputname.coor
velocities $inputname.vel ;# remove the "temperature" entry if you use
this!
extendedSystem $inputname.xsc
}

firsttimestep 0
binaryoutput no
restartfreq 500 ;# 500steps = every 1ps
restartname free_res
restartsave no
Binaryrestart yes

# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp

#temperature $temperature
# Periodic Boundary conditions

if {0} {
cellBasisVector1 67.410 0. 0.
cellBasisVector2 0. 40.470 0.
cellBasisVector3 0. 0 36.461
cellOrigin 22.001 2.315 -1.434
}

wrapWater on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 13.
switching on
switchdist 10.
pairlistdist 15

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#PME (for full-system periodic electrostatics)

PME yes
PMEGridSpacing 1

# Constant Temperature Control
if {0} {
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
}

# Constant Pressure Control (variable volume)
if {0} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# 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 100.
langevinPistonTemp $temperature
}

DCDfile free_more2.dcd
dcdfreq 250
velDCDfile free_more2.dcv
velDCDfreq 250
XSTfile free_more2.xst
XSTfreq 250

outputEnergies 100
outputPressure 100
outputtiming 200

# Minimization
if {0} {
minimize 20000
reinitvels $temperature
}

run 1500000 ;# 3ns

2. I have performed an equilibration on a complex system and found 6 h-bonds
in the equilibrated structure.Now I want to check their stability.Should I
perform another equilibration or free dynamics simulation? I myself perfer
the latter. Is that right?

Thank you very much for any help.

Best wishes,
Stanley

-- 
The future is now!

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:33 CST