From: Deva Priyakumar (deva_at_outerbanks.umaryland.edu)
Date: Thu Apr 13 2006 - 10:23:38 CDT
Hello,
I am a new user of NAMD. will somebody help me with this please.
My script looks something like this and the output follows. The VDW
energies are meaningless and I do not know where I am going wrong.
I checked the coordinates - they are fine.
The cell dimensions - i have checked and they are fine
when i turn of the periodic boundary conditions the calculation runs
fine.
Thanks
Deva
******************************************************************
# molecular system
coordinates erk_wat.pdb
structure erk_wat.psf
# force field
paratypecharmm on
parameters /raid/deva/parameters/par_all27_prot_na.prm
exclude scaled1-4
1-4scaling 1.0
# for periodic boundary conditions
# replace with your own box dimensions!
cellBasisVector1 47.7220001221 0.0 0.0
cellBasisVector2 0.0 34.2980003357 0.0
cellBasisVector3 0.0 0.0 32.171500206
cellOrigin -3.48490834236 -0.0266390871257 0.724303662777
wrapAll on
# you may use some other numbers.
PME on
PMEGridSizeX 100 # grid-pts along cellBasisVector1.
PMEGridSizeY 75 # along cellBasisVector2.
PMEGridSizeZ 75 # along cellBasisVector3
## use numbers with small integer factors: 2,3,5.
# approximations
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
# center-of-mass motion is automatically removed.
# integrator
timestep 1.0 # in fs.
stepspercycle 20
nonbondedFreq 2
# output
outputenergies 10
outputtiming 100
binaryoutput no
outputname test
dcdfreq 100 # how often we output trajectories.
# for restarting:
restartname ilb-min-restart
restartfreq 500
restartsave yes
binaryrestart yes # preserves more accuracy.
# no T or P coupling needed for EM.
temperature 0 # initial temperature
minimize 200 ; # steps to minimize
*************************************************************************
and the output:
Info: Entering startup phase 7 with 46866 kB of memory in use.
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.70577e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 6.62384e-17 AT 11.9974
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 9.09495e-13 AT 0.03125
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 4.21309e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.91168e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.16001e-17 AT 11.9974
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.98523e-22 AT 11.9974
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 8.0593e-16 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2.75 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 6656 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.055e-15 AT 0.0441942
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 7.45058e-09 AT
0.0441942
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 7.62939e-06 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
Info: Entering startup phase 8 with 50713 kB of memory in use.
Info: Finished startup with 53018 kB of memory in use.
TCL: Minimizing for 200 steps ETITLE: TS BOND
ANGLE DIHED IMPRP ELECT VDW
BOUNDARY MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE GPRESSURE
VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 10767.9627 12200.0122 1876.4167
2.2438 -105788.7202 -99999999.9999 0.0000 0.0000
0.0000 -99999999.9999 0.0000 -99999999.9999 -99999999.9999
0.0000 -99999999.9999 -99999999.9999 52657.3199 -99999999.9999
-99999999.9999
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:54 CST