From: Guna Mandava (guna.mandava_at_yale.edu)
Date: Wed Sep 16 2020 - 21:20:28 CDT
Hello,
I am simulating a protein on a gold surface with explicit waters in
order to determine the conformation of the protein on the surface, and
have thus applied periodic conditions to the xy direction, but not to
the z direction. The z direction is normal to the gold surface.
Because of this, I am using MSM (multilevel summation method) in order
to calculate long-range electrostatics rather than PME. I turned on
MSM, and I set the MSMzmin to -50 Å and the MSMzmax to 60 Å. For
context, my system is supposed to be in NVT and using measure minmax,
I get that the min z of the system that I set up is -45 Å and the max
z of the system is 45 Å.
When I try to equilibrate before the production run, I always get this
error after about 2-3 hours of simulation: Atom ----- is outside of
the MSM grid. The atom is always a TIP3P water, but for different
times I simulated it, I got different waters. The MSMzmin is fine,
because the surface is the z min, and the surface is fixed. My problem
is with water molecules reaching a z value > MSMzmax. Especially since
I am simulating in NVT with an MSMzmax that is in theory >10 Å larger
than the highest z value, this is confusing to me.
If someone has a .conf file that implements MSM successfully (without
the aforementioned error) in an NVT ensemble, that would be great.
My conf file is below for reference:
--------------------------------------------------------------------------------------------------------
############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ../omcs_au_ox_wb.psf
coordinates ../omcs_au_ox_wb_c.pdb
#############################################################
###RESTART OPTIONS ##
#############################################################
set inputname ../omcs_au_ox_min
set outputname omcs_au_ox_fixedprot
set temperature 310
firsttimestep 0
bincoordinates $inputname.restart.coor
#binvelocities $inputname.restart.vel # We are specifying temp here
extendedSystem $inputname.restart.xsc
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
#input
paraTypeCharmm on
parameters /home/gm555/project/parameters/updated/par_all36_prot.prm
parameters
/home/gm555/project/parameters/updated/toppar_water_ions_modified.prm
parameters
/home/gm555/project/parameters/updated/heme_charmm36_aa_orig.prm
parameters /home/gm555/project/parameters/updated/par_all22_prot.prm
parameters /home/gm555/project/parameters/updated/par_all22_prot_metals.inp
temperature $temperature
## NOTE: Do not set the initial velocity temperature if you
## have also specified a .vel restart file!
cellBasisVector1 99.6 0.0 0.0
cellBasisVector2 0.0 154.2 0.0
#cellBasisVector3 0.0 0.0 98.5
cellOrigin 0.00 0.00 0.00
#}
#
#}
wrapWater on
COMmotion off # disable initial center of mass motion
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds water ;#
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME (for full-system periodic electrostatics)
#if {1} {
#PME yes
#PMEGridSizeX 81
#PMEGridSizeY 144
#PMEGridSizeZ 100
#}
#MSM (multilevel summation method for electrostatics)
MSM yes
MSMzmin -50
MSMzmax 60
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Constant Pressure Control (variable volume)
#if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water bred, yes for membrane
useConstantArea no ;# no for water bred, yes for membrane
#}
langevinPiston off
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 50.
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 5000 ;# 5000steps = every 5ps
dcdfreq 5000 ;# change them back to 5000
xstFreq 5000
outputEnergies 5000
binaryoutput no ;# gives the pdb instead of the .coor
# Fixed Atoms Constraint (set PDB beta-column to 1)
#if {0} {
fixedAtoms on
fixedAtomsFile fixed_atoms.pdb
fixedAtomsCol B
#}
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
#if {0} {
#minimize 100
#reinitvels $temperature ;# the temperature statement above
verforms vel reassignment
#}
# change it back to 500000 for 500ps run
run 1000000 ;# 500ps run
------------------------------------------------------------------------------------------------------------------------------
For further context, the fixed_atoms.pdb holds every atom that is not
water fixed. Only waters are able to move.
Thanks,
Guna
Yale University
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