From: felmerino_at_uchile.cl
Date: Thu Sep 02 2010 - 10:30:55 CDT
Hi,
This is a VMD utility and VMD has its own mail list. Take a look at the VMD userguide (the measure command) http://www.ks.uiuc.edu/Research/vmd/current/ug/node133.html
there it is explained how to use the gofr from the command line which is pretty much the same as the gui. I suppose that the cell dimensions are stored in your dcd.
best
felipe
----Mensaje original----
Fecha: 02-09-2010 05:34
Para: "namd"<namd-l_at_ks.uiuc.edu>
Asunto: namd-l: g(r) calculation for CNT
Hi All
I ran CNT in water.it's conf file:
set temperature 300
firsttimestep 0
paraTypeCharmm on
parameters D:/par_nanotubes.inp
temperature 300
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 9.
switching on
switchdist 7.
pairlistdist 10.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 42. 0. 0.
cellBasisVector2 0. 44. 0.
cellBasisVector3 0. 0 47.
cellOrigin 0. 0. 0.0
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 32
PMEGridSizeY 32
PMEGridSizeZ 32
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 250 ;# 250steps = every 2ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 150000
reinitvels $temperature
run 1000000 ;# 5ps
for calculate g(r); I load dcd file but I don't know how I set the parameters in radial distribution function window.
qestions:
1- in "utilities" : should I put cell size from my config file?
2- in "selection1" & "selection2": what should I do?
my system is only carbonnanotube in water
3- in it's default at "last"frame is "-1", what's it meanning?&about delta r and max. tr too?
thank you
Sara
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