From: Frank Haverkort (f.haverkort_at_rug.nl)
Date: Wed Aug 28 2013 - 05:23:49 CDT
Hi,
I'm trying to minimize a box of dye molecules in water using the Charmm
Drude force field. However, I get the error:
FATAL ERROR: FOUND ISOLATED LONE PAIR PARTICLE 1503
Also, in the "structure summary" section of NAMD's standard output, the
stated number of bonds in the system is too low by exactly the number of
bonds to lone pairs (these lone pairs belong to the SWM4-NDP water). It
thus seems that bonds to lone pairs are not recognized by NAMD.
To solve this problem, I tried changing "drude off" into "drude on" in
the configuration file, since I think lone pairs are part of the charmm
Drude FF but not of the nonpolarized charmm one. However, I then got an
error message that stated I needed a Langevin thermostat, and when I
also added lines for a Langevin thermostat in the configuration file, I
got a new error message stating you can't minimize and use the langevin
thermostat simultaneously. So this turned out to be a dead end.
In another attempt at trying to figure out what was wrong, I ran a
normal MD simulation with exactly the same psf and pdb files as in the
minimization (with very small time step of 0.1 fs to account for the
missing minimization). This simulation ran without problems, so my psf
and pdb files are apparently OK.
I have no clue what else to try, and would appreciate any possible help!
The best,
Frank
This is the configuration file that I use:
minimization on
set boxsize 60.0
#input files
coordinates box_all.pdb
structure box_all_with_polarizability.psf
parameters charmm_drude_c36_aug12.prm
paraTypeCharmm on
#output file (section 3.2.2)
outputname out #specifies the prefix for the output files
binaryoutput no #activates binary output (yes=binary)
outputenergies 100 #number of timesteps between energy output
# integrator params
firsttimestep 0 # Starting time of the simulation.
rigidBonds water
useSettle on
# force field params
seed 12345
waterModel swm4
exclude 1-3
switching on # Use a switching function to truncate the van der
Waals potential energy smoothly at the cutoff distance.
switchdist 10.5
cutoff 12.0 # For van der Waals and electrostatic forces.
pairlistdist 13.5
fullElectFrequency 4 # Number of timesteps between evalutations of
long-range electrostatic forces. MODIFY WHEN TIMESTEP LARGER THAN 1 FS
IS USED.
longSplitting c2 # Method to split electrostatic forces in short range
and longe range part.
# drude
drude off
# periodic cell
cellBasisVector1 $boxsize 0 0
cellBasisVector2 0 $boxsize 0
cellBasisVector3 0 0 $boxsize
# long-range electrostatics
PME yes
PMEGridSpacing 1.0
FFTWUseWisdom no # This can be turned on later, when using the same
size PME grid multiple times, to reduce startup time.
minimize 10000
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