Re: Rattle Error During Equilibration of Lipid Bilayer Membrane

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Sat Feb 11 2006 - 09:49:07 CST

Hi,

It seems to me that you don't have periodic boundary for your system, and once you build that you have to make PMEGridSize to be >= 1.5 of the length of that axis.

I hope that will fix your problem.



Morad Alawneh

Department of Chemistry and Biochemistry

C100 BNSN, BYU

Provo, UT 84602



Arneh Babakhani wrote:
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 





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