From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Feb 13 2004 - 12:51:50 CST
Hi Amarda,
For practical stuff...
Have you looked at the tutorials on the NAMD website? Some pretty fancy
stuff is detailed there to get people going.
Depending on how deep you want to learn MD, several texts are available
one of the better ones is written by Andrew Leach--Molecular Modelling.
Pestering the list will work for awhile, but even I have been known to get
people uptight real quick.
In your case a few detailed hints might get you through this first step.
First, check the minimization logs and make sure that the water and ions
have settled down. The keyword here is the electrostatic and vdw
energies should stabilize when minimization is good.
Second, minimization the whole system to get the protein-solvent
interface optimized.
Third, heat slowly!!! I am assuming that your heating was occuring in one
times step. This will definitely cause rattle to wail..
finally if possible, post logs and config files to the list to aid in
troubleshooting (less pestering will be needed).
Brian
On Fri, 13 Feb 2004, Amarda Shehu wrote:
>
>
> Yes, I know, 1000 seems too high. Basically I am trying to make somebody's
> config files work. I am told to prepare a protein system for a full md
> simulation and having no previous experience with namd or md simulations,
> am following somebody's steps in equilibrating the system to get it ready
> for the md simulation.
>
> I first minimized the waters and the ions leaving the
> protein fixed. Now I'm trying to heat the solvent. Should I try a
> different lower temperature? As a grad student in Comp. Science, I have
> found very little practical information on how to conduct md simulations.
> Do you now of any source besides pestering people in the newsgroup?
>
> Thank you,
> Amarda Shehu.
>
> On Thu, 12 Feb 2004, Brian Bennion wrote:
>
> > Hello Amarda,
> >
> > I don't mean to be incipeint but a 1000K or degrees is a bit extreme
> > especially if at the previous timestep the temp is 0 Kelvin. The rattle
> > algorithm wasn't built for those velocities. In fact a lot a minimization
> > is needed when solvent has been placed around a protein or ions for that
> > matter. Having said all that, you can turn it off if you want.
> >
> > Brian
> >
> >
> > On Thu, 12 Feb 2004, Amarda Shehu wrote:
> >
> > >
> > > Does anyone know how to deal with constraint failures in the RATTLE
> > > algorithm? I have been trying to heat up the solvent with ions for a
> > > protein system that is fixed, temperature set to 1000. However, I have had
> > > continuous problems with certain atoms shaking too much and the whole
> > > system becoming unstable. I thought doing some minizations to equilibrate
> > > the system on the fly would do the trick. However, it seems that there is
> > > always one atom (not the same one, varies from simulation to simulation)
> > > that destabilizes the system. Do I need more minizations?
> > > I have checked that my system is well inside the bounding box.
> > >
> > > Does anyone have any word of direction?
> > >
> > > Thank you,
> > > Amarda Shehu.
> > >
> > > Computer Science Department,
> > > Rice University.
> > >
> >
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
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