Pressure profile calculation problem

From: wenchangyu2006_at_gmail.com
Date: Tue Mar 23 2010 - 15:38:56 CDT

Dear all,
When I do pressure profile calculation on membrane protein system, I tried
several times to make namd running without errors but also without any
output. I'll paste my config file in the follwing. I appreciate any
suggestions, thanks.

######## config file ########

# --- integration ---
timestep 2.0
temperature 310

# --- input files ---
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
structure pp.xpsf
coordinates pp.coor
extendedSystem pp.xsc

# --- output files ---
binaryoutput no
outputname pp-out

# --- constraints ---
rigidBonds all
rigidTolerance 0.00000001
rigidIterations 100
useSettle on

# -- non-bonded interactions ---
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10
cutoff 12
dielectric 1.0
PME yes
PMEGridSizeX 150
PMEGridSizeY 150
PMEGridSizeZ 180

# --- non-bonded list ---
stepspercycle 10
pairlistdist 14

# --- pressure profile calculation
pressureProfile on
pressureProfileSlabs 50
pressureProfileFreq 1
pressureProfileAtomTypes 6
pressureProfileAtomTypesFile all.pdb
pressureProfileEwald on
pressureProfileEwaldX 16
pressureProfileEwaldY 16
pressureProfileEwaldZ 16

set ts 5000

coorfile open dcd pp_10ns.dcd
while { [coorfile read] != -1 } {
firstTimestep $ts
run 0
incr ts 5000
}

coorfile close

###### output from namd
.............
Info: Entering startup phase 8 with 163825 kB of memory in use.
Info: Finished startup with 173253 kB of memory in use.
Info: Coordinate file pp_10ns.dcd opened for reading.
Info: Reading timestep from file.
Info: Updating unit cell from timestep.
Info: REMOVING COM VELOCITY 0.000607021 -0.0171051 0.00104308
TCL: Setting parameter firstTimestep to 5000
TCL: Running for 0 steps

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