From: Cetin Baloglu (baloglu_at_gmail.com)
Date: Mon Apr 25 2005 - 03:22:11 CDT
Dear All,
I have 2ns trajectories of lysozyme at different temperatures, (my
input file is below for 315K) . After extracting the total energies, I
try to get the heat capacity at each temperature. This way I want to
see the transition points, but what I have with <(E-<E>)^2>/k(b)T^2
function is always similar values giving me a horizantal line in heat
capacity versus temperature graphics. But this result does not fit
with the previous results. I want to ask if my input file is ok for
the heat capacity calculations.
Is there a better way to calculate such calculations? I also want to
calculate relaxation functions, I wonder if any of you has experience
on such calculations or offer me a software for this.
#>>> INPUT FILES
set TEMP 315
coordinates lyz_315_eq.coor
structure lysozyme.psf
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
#>>> OUTPUT FILES
outputname lyz_315
binaryoutput no
DCDfile lyz_315.dcd
DCDfreq 1000
#>>> STANDARD OUTPUT
outputEnergies 1000
outputMomenta 0
outputPressure 0
outputTiming 0
#>>> TIMESTEP PARAMETERS
numsteps 1
timestep 2.0
rigidBonds all
#nonbondedFreq 2
#fullElectFrequency 6
useFlexibleCell no
useConstantArea no
LangevinPiston off
stepspercycle 20
#>>> SIMULATION SPACE PARTITIONING
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
cellBasisVector1 48.0 0 0
cellBasisVector2 0 45.0 0
cellBasisVector3 0 0 54.0
cellOrigin 0.73 22.08 19.69
wrapWater on
PME on
PMEGridSizeX 48
PMEGridSizeY 45
PMEGridSizeZ 55
useGroupPressure yes
#>>> BASIC DYNAMICS
exclude scaled1-4
temperature $TEMP
1-4scaling 1.0
seed 12345
langevin off
langevinDamping 1.0
langevinHydrogen off
langevinTemp $TEMP
tcouple on
tcoupletemp $TEMP
tcouplefile prefix.pdb
tcouplecol B
run 1000000
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