Re: atoms moving fast

From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Sat Sep 08 2007 - 10:22:53 CDT

Either set 'rigidbonds all' or set your timestep to 1fs.
You can consult the NAMD paper (Philips et al. 2005) for references on
constraining the bonds to hydrogens.

Victor

On Sat, 2007-09-08 at 08:31 -0500, Xiang Mao wrote:
> Hello, everyone:
> I met some problem when I continue my MD. The error message
> is atoms moving too fast. After minimize the system, I equilibrated
> the system for 100ps, no problem at all, I set temperature to 310, the
> average temperature in the equilibrium is about 330K(I think it might
> be ok). But when I try to do MD further, the temperature keeps going
> up. And when it goes to another 36ps, the MD stop, and got the error
> message. I have check the last coordiation of the protein, and that
> specific atom, all of them are ok. Attached is my config file. I am
> wondering if someone could give me some suggestion about my problem. I
> really appreciate it.
>
> Best,
> mao
>
> structure solvate.psf
> coordinates pep_wat_eq.coor
> velocities pep_wat_eq.vel
> extendedSystem pep_wat_eq.xsc
> parameters par_all27_prot_lipid_na.inp
> paraTypeCharmm on
>
> outputEnergies 1000
> outputTiming 1000
> xstFreq 1000
> dcdFreq 1000
> restartfreq 1000
> wrapAll on
> wrapNearest on
>
> timestep 2
> nonBondedFreq 2
> fullElectFrequency 4
> stepsPerCycle 20
>
> switching on
> switchDist 12
> cutoff 14
> pairlistdist 16
>
> # Periodic Boundary Conditions
> cellBasisVector1 75.44 0. 0.
> cellBasisVector2 0. 66.46 0.
> cellBasisVector3 0. 0 97.63
> cellOrigin -21.99 -15.72 -32.98
>
>
> # the z dimension is going to shrink so pad sufficiently
> # the margin could be reduced once the cell is equilibrated
> # margin 2
>
> Pme on
> PmeGridsizeX 128
> PmeGridsizeY 128
> PmeGridsizeZ 128
>
> exclude scaled1-4
> 1-4scaling 1.0
> COMmotion no
> dielectric 1.0
>
> # use lighter damping now that system is equilibrated
> langevin on
> langevinDamping 1
> langevinTemp 310
> langevinHydrogen no
>
> # use lighter damping now that system is equilibrated
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 200
> langevinPistonDecay 500
> langevinPistonTemp 310
>
> useGroupPressure yes
> useFlexibleCell no
> useConstantRatio no
> outputname pep_wat
>
> firsttimestep 50000
> run 500000
>
>
>
>

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