AMBER Archive (2003)

Subject: Re: AMBER: pair-cutoff

From: David A. Case (case_at_scripps.edu)
Date: Tue Sep 23 2003 - 10:59:01 CDT

On Tue, Sep 23, 2003, nie beining wrote:
>
> I found from reference that pair-cutoff was used in GROMACS simulation
> package, that is, short-range cutoff for all non-bonded interactions,
> long-range cutoff for electrostatic interaction calculated in larger
> time steps. I am wondering if Amber is capable to do so. Is there
> anyone who has dealt with this issue before?
>

The "nrespa" variable allows you to carry out the reciprocal part of the Ewald
procedure (roughly, the long-range part of electrostatics) at intervals, while
continuing to evaluate short-range interactions every step.

For most biomolecular systems, using the default direct-space cutoff of
8 Ang, nrespa=2, dt = 0.001 to 0.002 ps works pretty well, giving acceptably
small fluctuations and drift in total energy, while being reasonably
efficient.

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