ERROR in multiple walker metadynamics simulation

From: Miyu Tamura (tamura.miyu_at_d.mbox.nagoya-u.ac.jp)
Date: Tue Aug 21 2018 - 01:30:09 CDT

Dear All,

I am trying to perform 2-dimensional multiple walker metadynamics
simulations for the permeation of the drug molecule across the lipid
membrane.
I have used the position of the drug molecule along the bilayer normal (Z)
and the tilt angle of the drug molecule with respect to the bilayer normal
as reaction coordinates.

But after 1000 steps of minimization, the simulation crashes and I get the
following error.

ERROR: Constraint failure in RATTLE algorithm for atom 20!
ERROR: Constraint failure; simulation has become unstable.

I am using NAMD2.12 and only a rigid part of the drug molecule to compute
the tilt variable.
The input is as follows.

colvar {
   name Zdistance
   width 0.5

   lowerboundary 0.0
   upperboundary 36.0
   lowerwallconstant 10.0
   upperwallconstant 10.0

   distanceZ {
      oneSiteSystemForce on
      main {
         atomNumbersRange 1 - 32
      }
      ref {
         atomsFile ../reference.pdb
         atomsCol B
      }
   }
}

colvar {
   name angle
   width 0.1

  lowerboundary -1.0
  upperboundary 1.0

  extendedLagrangian on
  extendedFluctuation 0.001
  extendedTimeConstant 200

  tilt {
    axis (0.0, 0.0, 1.0)
    atoms {
      atomNumbers { 1 2 6 19 8 4 }
    }
    refPositionsFile ./tilt.ref
  }
}

metadynamics {
   name meta
   colvars Zdistance angle
   hillWeight 0.01
   newHillFrequency 1000
   dumpFreeEnergyFile yes
   writeHillsTrajectory on

   multipleReplicas yes
   replicaID rep1
   replicasRegistry replicas.registry.txt
   replicaUpdateFrequency 10000
}

#############################################################
## JOB DESCRIPTION ##
#############################################################
structure ionized.psf
coordinates slabZ32.pdb

extendedSystem initial.xsc
set temperature 310.
temperature $temperature
firsttimestep 0

#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters ./../../common/par_all36_lipid.prm
parameters ./../../common/par_all36_cgenff.prm
parameters ./../../common/toppar_water_ions_namd.str

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.0
pairlistdist 14.0
margin 5.0
vdwForceSwitching on

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# Needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 310.
langevinHydrogen off ;# don't couple langevin bath to hydrogens

# Periodic Boundary Conditions
cellOrigin 0. 0.0 0.0
wrapWater on

# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 72
PMEGridSizeY 72
PMEGridSizeZ 80

# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell yes
useConstantRatio yes

langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.
langevinPistonDecay 100.
langevinPistonTemp 310.

#############################################################
## EXTRA PARAMETERS ##
#############################################################
## Colvars
colvars on
colvarsConfig rep1.in
#colvarsInput $inputname.colvars.state

#############################################################
## EXECUTION SCRIPT ##
#############################################################
#Minimization
minimize 1000
reinitvels 300
run 25000000 ;# 50 ns

Do you have any idea why this happens?
Any advice you could provide me would be greatly appreciated

Thank you,
Miyu Tamura

This archive was generated by hypermail 2.1.6 : Wed Sep 18 2019 - 23:20:15 CDT