AMBER Archive (2005)

Subject: RE: AMBER: molecule blowing apart during equilibration

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Feb 18 2005 - 10:56:30 CST


Dear Julie,

> in a lattice is blowing apart at the equilibrium stage. The
> output of the
> equilibration
> follows. Is it obvious which parameter blows up first? Can

> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> NSTEP = 1 TIME(PS) = 0.005 TEMP(K) =
> NSTEP = 2 TIME(PS) = 0.010 TEMP(K) =

You are taking a 5fs time step. This leads to integration errors and will
prevent you from obtaining a stable trajectory. Typically if you use shake
on hydrogens you require a time step of 2fs or shorter. Without shake you
need 1fs or shorter.

Try it with a 1fs time step (dt=0.001) and the simulation should be fine.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu