AMBER Archive (2003)

Subject: Re: lanes when solvating in LEAP (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Fri Mar 07 2003 - 11:56:39 CST

On Fri, Mar 07, 2003, amber_at_heimdal.compchem.ucsf.edu wrote:
>
>
> when we solvate in LEAP with a non-water solvent and more than one box is
> needed to solvate, some strange lanes between solvent boxes appear in the
> final system. I think that this is due to the unproper definition of the
> closeness parameter for the NEW solvent.
>
> i) is this behaviour normal??

Yes.

> ii)is it somehow avoidable??

Only by changing the code. The idea is that these initial infelicities will
go away upon equilibration.

..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
==================================================================