From: Mert Gür (gurmert_at_gmail.com)
Date: Wed May 13 2009 - 10:06:55 CDT
Hi everyone,
I am a quite new user of Linux. I have performed a number of MD simulations.
What I am searching for is the energy of only the protein.
I have read the linux tutorial of namd and also read the corresponding
e-mails in this list.
My problem is that the way I have written my get-energy.conf file either
does not work properly or does not give me the energy of only the protein.
I came to this conclusion by comparing the energies both with the ones I
have obtained via vmd's namdenergy plugin (in windows) and via mdenergy
For example in linux I obtained
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
ENERGY: 3039000 126.4302 379.9730 174.6389
23.0378 -57317.3079 5216.9948 0.0000 0.0000
10013.9117 -41382.3216 301.2902 -41358.1629
-41358.1629 301.2902 -976.4120 -943.0767
178158.8790 -976.4120 -943.0767
whereas in windows I have obtained (which is also close to mdenergy's
result)
Frame Time Bond Angle Dihed
Impr Elec VdW Conf Nonbond
Total
0 0 +126.308 +405.648 +188.96
+17.5462 -476.427 -122.028 +738.463 -598.456
I attached my file in case you are interested. I used 1EJG crambin in my
simulation so the name of the file is correspondingly different.
Any help or even an example ..-get-energy.conf file would be appreciated.
Mert
structure ../common/1EJG_wb.psf
coordinates ../common/1EJG_wb.pdb
binCoordinates ../run4/res.coor
binVelocities ../run4/res.vel
extendedSystem ../run4/res.xsc
set temperature 300
set outputname 1EJG
set restartname res
firsttimestep 3039000
# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# Integrator Parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen off
## Periodic Boundary Conditions
cellBasisVector1 57.9 0. 0.
cellBasisVector2 0. 53.7 0.
cellBasisVector3 0. 0. 57.3
cellOrigin 11.2 10.0 6.3
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 60
PMEGridSizeY 54
PMEGridSizeZ 60
# Output
outputName $outputname
restartName $restartname
outputEnergies 500
outputPressure 500
restartfreq 500
dcdfreq 500
xstFreq 500
# runs 0 time steps for each frame in the dcd
# opens the dcd file to read the coordinates
coorfile open dcd 1EJG-prot.dcd
set i 0
while { ![coorfile read] } {
incr i 500
firsttimestep $i
run 0
}
coorfile close
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:47 CST