From: Pang, Yui Tik (andrewpang_at_gatech.edu)
Date: Sat Jan 30 2021 - 11:19:21 CST
I suspect NAMD did not recognize the LP correctly. If you look into your psf file, do you find a line like … !NUMLP NUMLPH ? What does that line and the following line says?
From: Seke Keretsu<mailto:sekekeretsu_at_gmail.com>
Sent: Saturday, January 30, 2021 1:54 AM
Subject: namd-l: Dealing with lone pairs (LP) during simulation
I came across the following error during the equilibration of my protein ligand system which has a CL atom (in ligand). I prepared the system using CHARMMGUI
ERROR: Atom 4737 velocity is -11982.1 12908.1 -3406.91 (limit is 12000, atom 983 of 1008 on patch 17 pe 1)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 17 pe 1).
Here, the atom no. 4737 corresponds to the lone pair connected to CL atom in the system.
I have checked the mailing list which suggested to perform the simulation gradually from low temperature for atoms moving fast. However, I could not find a solution for dealing with lone pairs. I keep getting the same error regardless of the temperature.
Is there a command I need to give in the configuration file?
Please give me some advice or link to a solution.
The configuration file used during equilibration is given below.
set temp 50;
set outputname equilibration03;
set inputname equilibration;
restartfreq 1000; # 1000 steps = every 2ps
dcdUnitCell yes; # the file will contain unit cell info in the style of
# charmm dcd files. if yes, the dcd files will contain
# unit cell information in the style of charmm DCD files.
xstFreq 5000; # XSTFreq: control how often the extended systen configuration
# will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
# The number of timesteps between each energy output of NAMD
outputTiming 1000; # The number of timesteps between each timing output shows
# time per step and time to completion
# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter file(s)
# multiple definitions may be used but only one file per definition
# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are bonded are going to be ignored
# 1-3: 3 consecutively bonded are excluded
# scaled1-4: include all the 1-3, and modified 1-4 interactions
# electrostatic scaled by 1-4scaling factor 1.0
# vdW special 1-4 parameters in charmm parameter file.
vdwForceSwitching yes; # New option for force-based switching of vdW
# if both switching and vdwForceSwitching are on CHARMM force
# switching is used for vdW forces.
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
# switchdist - where you start to switch
# cutoff - where you stop accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
# cycle represents the number of steps between atom reassignments
# this means every 20/2=10 steps the pairlist will be updated
# Integrator Parameters
timestep 1.0; # fs/step
rigidBonds all; # Bound constraint all bonds involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step
# Constant Temperature Control ONLY DURING EQUILB
reassignFreq 500; # reassignFreq: use this to reassign velocity every 500 steps
cellBasisVector1 69.61299896240234 0 0
cellBasisVector2 0 76.30400085449219 0
cellBasisVector3 0 0 74.61400032043457
cellOrigin 12.257286071777344 7.4436726570129395 -19.06593894958496
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
#wrapNearest $wrapnearst; # use for non-rectangular cells (wrap to the nearest image)
# PME (for full-system periodic electrostatics)
PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size
# Pressure and volume control
useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and
# has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for anisotropic system like membrane
useConstantRatio yes; # keeps the ratio of the unit cell in the x-y plane constant A=B
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