Re: Re: too much rattle

From: Amarda Shehu (shehua_at_cs.rice.edu)
Date: Fri Feb 13 2004 - 12:24:12 CST

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 **
> *****************************************************************
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:04 CST