RE: High VDW energies during minimization and dynamics

From: Pijush Ghosh (pijush.ghosh_at_ndsu.edu)
Date: Thu Apr 13 2006 - 11:52:35 CDT

Hello Deva,
 As far as your script goes I don't see any problem except ' paratypecharmm
on' which should be 'paratypeCharmm on'. I am afraid if because of this NAMD
is not able to read your parameter file. So please check this. Also make
sure that your box size is not too tight, leading to system instability at
the very beginning, giving weird 999999999999.0000 values for your energy.

Hope, I haven't confused your further.
Goodluck.

Pijush Ghosh
PhD Student
Department of Civil Engineering
North Dakota State University
Fargo. ND. 58105. USA
Phone:
     701-231-6491(Lab)
     701-231-4341(Res)

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Deva Priyakumar
Sent: Thursday, April 13, 2006 10:24 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: High VDW energies during minimization and dynamics

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

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