From: Pegah Khalili (pegahk5_at_gmail.com)
Date: Wed Nov 03 2010 - 04:28:59 CDT
Dear All,
I am new to NAMD and am having some problems with using a suitable
temperature control algorithm for my system.
My system involves heating, equilibrating and running dynamics on
cyclodextrins in a waterbox with periodic boundary conditions, using the NPT
ensemble. I am currently testing this for alpha-cyclodextrin.
I have run equilibration (1ns) and dynamics (100ns) on alpha-cyclodextrin
using Langevin dynamics for temperature and pressure control, but the
temperature and energy fluctuations are high during the simulation (temp.
fluctuates between 290-305K, and energy fluctuates between -32400 and -31800
kcal/mol - is this normal?).
Also, the time correlation functions I generate using the 100ns simulations
do not decay exponentially like they should - I think this is due to using
the Langevin dynamics method for temperature control, but I am not sure.
Would anyone be able to help me with this problem. Do I need to use a
different method for temperature and pressure control? Is this causing
problems with the correlation functions?
Thank you in advance.
I have included a copy of my dynamics input script below:
set temperature 298.15
#numsteps 100
dielectric 1.0
#firsttimestep 0
if {1} {
set inputname ACD_whed-1
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel
extendedSystem $inputname.xsc
}
coordinates ACD_whed-1.coor
outputname ACD_whed-2
outputEnergies 100
binaryoutput no
DCDFreq 100
restartFreq 100
#temperature $temperature
structure acd_water_heat_xpl.psf
paraTypeCharmm on
parameters par_all22_prot.inp-kjn-map
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.0
pairlistdist 14.0
seed 27041994 ;#seed value
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
rigidTolerance 1.0E-10
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
if {0} {
cellBasisVector1 49.8129 0. 0.
cellBasisVector2 0. 49.8129 0.
cellBasisVector3 0. 0. 49.8129
cellOrigin -0.0207 -0.0727 -0.0403
}
wrapWater on
wrapAll on
if {1} {
PME yes
PMEInterpOrder 6 ;# interpolation for B-spline
PMEGridSizeX 54
PMEGridSizeY 54
PMEGridSizeZ 54
PMETolerance 4.6809305e-9 ;# corresponds to a KAPPA value of 0.32
}
if {1} {
useGroupPressure yes
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
}
#minimize 1000
#reinitvels $temperature
run 500000 ;# 500ps
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:19 CST