Rattle Error During Equilibration of Lipid Bilayer Membrane

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Feb 10 2006 - 22:32:51 CST

Dear NAMD community,

I constructed and solvated a lipid bilayer membrane. This consists of
200 DMPC lipids (100 per monolayer), about 5100 water molecules, for
a total of ~40,000 atoms.

I conducted 10,000 steps of minimization, ultimately achieving a
gradient tolerance of ~2.91. At the end of this minimization, I zeroed
the velocities of all atoms. No problem here . . .

I then gradually heated up my system, over 2500 steps (2fs timestep), to
330K. Looking at the plot of the temperature, the system does heat up
gradually, eventually plateauing out at 330K, towards the end of the
run. No problem here . . .

I then turn on constant pressure and attempt to run for another 2500
steps. The temperature spikes from 330K to ~375K, by the second step!
(I am implementing langevin temp control). The temp. gradually
decreases through the course of the simulation, but it never quite gets
back down to 330K. NAMD prematurely aborts halfway through the run, at
about 350K, giving the following error:

ERROR: Constraint failure in RATTLE algorithm for atom 13561!

ERROR: Constraint failure; simulation has become unstable.

ERROR: Exiting prematurely.

I found through some trial & error that by increasing the langevin
Damping parameter, I can decrease the magnitude of this initial
temperature spike (although I can't get rid of it completely, very
strange). By decreasing this spike, the system comes back down to 330K
much faster, and the simulation proceeds to completion (with langevin
Damping = 7).

I then try to run a 1 ns equilibration of my membrane, again using lang.
Damping = 7 (since this seemed to work for the constant pressure run).
This runs for about 850 ps and then aborts, with the same RATTLE
algorithm error. However, during this equilibration, the temp. stays
constant, as does the pressure (no spikes), and nothing else is
observably wrong. I repeated the attempt for lang. Damping =5, and 9,
no joy, still aborts.

Would greatly appreciate any ideas? (I've pasted my conf file below for
reference)

Regards,

Arneh

#############################################################
# 1NS equilibration dmpc lipid bilayer in a Water Box
#############################################################
structure ../common/solvated.psf
coordinates ../common/solvated.pdb
bincoordinates lipwaterconstpress2.coor
binvelocities lipwaterconstpress2.vel
extendedsystem lipwaterconstpress2.xsc

set temperature 330
set outputname lipwaterequil1

firsttimestep 0

## SIMULATION PARAMETERS ##

paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 10.
switching on
switchdist 9.
pairlistdist 11.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 7 ;# damping coefficient (gamma) of 9/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens

wrapAll on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 64
PMEGridSizeY 64
PMEGridSizeZ 64

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.
langevinPistonDecay 200.
langevinPistonTemp $temperature

# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
outputEnergies 100
outputPressure 100

run 500000 ; # 1ns

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:15 CST