From: Sascha Tayefeh (sascha_at_pc.chemie.tu-darmstadt.de)
Date: Tue Aug 30 2005 - 01:26:25 CDT
Hi!
It is very likely, that your system is still not relaxed sufficiantly
to start a simulation. There could be several reasons, e.g. unsatisfied
force-field restraints, wrong boundary conditions and many more.
First, I'd give a smaller stepsize a try:
timestep 0.1
then a much lower temperature, e.g. 1K. If all this does not work, try
a higher dcdfreq (since I assume your simulation crashed earlier than
100 steps), e.g.:
dcdfreq 10
and have a look at the trajectory, maybe using VMD. Watch atom 47. It
is supposed to move much faster. Try to find out why and you're much
closer to solve your problem.
Sincerly
S.T.
Phoenix schrieb:
> Hi all,
> I got a problem when I heating a system to 298k.After I minimize the
> system in
> 10000 steps keeping the protein fixed and allowing the movement of the
> water
> box.I want to heat the system to 298k in 20000 steps and occur the
> problem.How could I do to solve the problem? attched is my config file
>
>
> ERROR: Atom 47 velocity is 14541.4 -2450.69 -6229.53 (limit is 10000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
>
>
>
> ------------------------------------------------------------------------
>
> cwd /iodisk1/home/wujh/md/heat
>
>
> # molecular system
>
>
> structure /iodisk1/home/wujh/md/ionized.psf
> coordinates /iodisk1/home/wujh/md/heat/miniout.coor
>
>
>
> # force field
> paratypecharmm on
> parameters /iodisk1/home/wujh/md/par_all27_prot_lipid.inp
>
> exclude scaled1-4
> 1-4scaling 1.0
>
>
> # Restart Control
> firsttimestep 0
> binaryoutput no
> restartname PSEres
> restartsave no
> restartfreq 1000
> Binaryrestart yes
>
>
> # approximations
> switching on
> switchdist 8
> cutoff 12
> pairlistdist 15
> stepspercycle 10
>
> #integrator
> timestep 1.0
>
>
> #output
> outputenergies 10
> outputtiming 100
>
>
> cellBasisVector1 79.672 0.0 0.0
> cellBasisVector2 0.0 84.715 0.0
> cellBasisVector3 0.0 0.0 161.068
> cellOrigin -4.58 -8.01 75.00
>
>
> wrapAll on
> wrapWater on
>
> PME yes
> PMEGridSizeX 80
> PMEGridSizeY 90
> PMEGridSizeZ 180
>
> temperature 0
> reassignFreq 200
> reassignTemp 10
> reassignIncr 10
> reassignHold 298
>
> #fixatoms
> fixedAtoms on
> fixedAtomsForces off
> fixedAtomsFile /iodisk1/home/wujh/md/heat/fixed.pdb
> fixedAtomsCol B
>
>
> #output
> outputname heatout
>
>
> #protocol
> DCDfile heatout.dcd
> dcdfreq 100
> velDCDfile heatout.dcv
> velDCDfreq 100
> XSTfile INTdcd.xst
> XSTfreq 100
>
>
> run 20000
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