AMBER Archive (2003)

Subject: Re: AMBER: large changes in xyz coordinates

From: David A. Case (case_at_scripps.edu)
Date: Sat Aug 16 2003 - 23:07:25 CDT

On Sat, Aug 16, 2003, Sivakolundu, Sivashankar wrote:

> I'm trying to do an constant pressure md simulation of a protein solvated in
> a water box using Amber 7 for several nanoseconds. The simulation went fine
> until it was around 8 ns and then it crashed without any error message. I
> couldn't restart the simulation since the restart file didnt seem to have
> any coordinates (see below), though the values for velocities looked fine.

You should certainly visualize your trajectory to see what is going on...
my guess is that some problem will be obvious, if all of the coordinates
are getting extremely large.

You set nscm to 0, which disables removal of center-of-mass translational
motion...it is probably better to leave this at its default value.

If the program crashed in the middle of a run (you don't say) I don't know
why that would happen. But it looks like somehow you generated some
translational motion in the system during equilibration, and never removed
any of it.

..hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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