> > > I heat the system step by step from 0 to 308 K
> > > for about 20 ps, after minimizition.
> >
> > Stepwise warming is good. How about NVT vs. NPT?
> > If you send your mdin files, we can check more
> > in detail. 20ps seems a little short for a big
> > system. Did you graph e.g. density and rms?
[My interest in equilibration was based on the impression
the problem occurred early in the simulation, but this was
not the case.]
> do you mean mdin files is this (the below lines)?
I meant the mdin files used to warm the system and bring the
density to the proper value. This appears to be a production
mdin:
> &cntrl
> imin = 0, irest = 1, iwrap=1 ,ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 308.0, temp0 = 308.0,
> ntt = 1, gamma_ln = 0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100, ntwx = 500, ntwr = 1000
> > > the below message came after 48 ns.
> > > also my system is a dimer protein with one ligand.
> >
> > I assume that's 48 ps?
>
> this message came after 48 ns.
This implies the system is equilibrated. What is the rms
of the solute to starting structure? Was there steady
divergence and a plateau, or some other pattern? Have
you graphed temperature, energy, and density? It might
be interesting to redo your last run saving every step
in mdout and mdcrd, and search for the start of the
problem.
> my jobs was a series of 200ps so after 240 run this message
> came.So the run 240 is stoped. and I also check the mdcrd
> from run 239 by VMD, I saw a long bond in one residue, which
> it didnt occure in run 238.
> What should I do for fixing the problem of defected bond?
How long? What atoms? Was one of the atoms getting unusually
close to a third atom? Sometimes atoms w/out vdw can get pulled
into other atoms and generate large forces.
> I should also said that I add iwrap=1 for getting 239.rst,
> and by adding this I saw that the xyz of the protein changes.
That shouldn't affect anything, but it would be interesting to
try the same run w/out iwrap, and see if the problem still
occurs. Also to try putting iwrap on the previous run and see
what happens.
> > In such cases the ligand parameterization is the main suspect,
> > but my impression is that usually it happens sooner if this is
> > the case.
The case of vdw-less fusion could take a while to occur if the
right atoms are not close at the outset. I am not familiar enough
with the force field these days to predict the likelihood.
> > Another possibility that occurs to me is that you might
> > be restarting with the wrong restrt file or mdin.
Less likely given how many runs you have made.
> I also run a simulation of the same system with 2 ligand (this
> was with one ligand), and it finished succesfully, so I think it
> not because of the parametrization of ligand.
Good point. It would have to be a rare interaction. Possibly
involving atom 606 or 607:
> > > vlimit exceeded for step 0; vmax = 388.4665
> > > vlimit exceeded for step 1; vmax = 399.4700
> > > vlimit exceeded for step 2; vmax = 387.9217
> > > vlimit exceeded for step 3; vmax = 352.8459
> > > vlimit exceeded for step 4; vmax = 32817.3873
> > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > deviation is too large
> > > NITER, NIT, LL, I and J are : 0 3 302 606 607
> > > Note: This is usually a symptom of some deeper
> > > problem with the energetics of the system.
> >
> > I think atoms 606, 607 are the problem here. One thing you could try
> > is to save every step to mdcrd and watch what happens in a dynamics
> > viewer like VMD.
Still a good idea :-)
> >
> > Bill
> >
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Received on Sat Jun 19 2010 - 10:00:03 PDT
