From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Aug 21 2018 - 09:05:31 CDT
This probably has nothing to do with metadynamics or your colvars - I would
equilibrate without either of those complications. Maybe check that your
box is large enough or that your system density is otherwise sensible.
HTH,
BKR
On Tue, Aug 21, 2018, 2:32 AM Miyu Tamura <tamura.miyu_at_d.mbox.nagoya-u.ac.jp>
wrote:
> 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
>
>
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