AMBER Archive (2005)

Subject: Re: AMBER: igb=10 some vdW terms disappear?

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Mar 22 2005 - 15:54:57 CST

Dave,

I find the single water molecule is before your chloroform molecules in
the prmtop file. This arrangement can trick the pb code to think there
is nothing after the water when it builds the nonbonded list ... so you
see chloroform molecules penetrating the solute. Please always put water
molecules at the very end, and try again.

All the best,
Ray

>-----Original Message-----
>From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
>Of Ray Luo
>Sent: Monday, March 21, 2005 5:15 PM
>To: amber_at_scripps.edu
>Subject: Re: AMBER: igb=10 some vdW terms disappear?
>
>Dave,
>
>Could you email me all input/data files so I can reproduce your problem
>with igb=10?
>
>Best,
>Ray
>
>Wells, David H wrote:
>
>
>
>>Web Bug from MailScannerWebBug
>>
>>In a system with 86 explicit chloroform molecules solvating a simple
>>organic molecule (c8h13n1o2) and a water molecule running md with
>>igb=10 I find chloroform molecules "penetrating" the organic molecule
>>as though van der Waals terms were being ignored. Simply changing
>>igb=10 to igb=0 eliminates the problem.
>>
>>
>>
>>The unit checks out cleanly with xLeap prior to saving parm & coord
>>
>>
>files.
>
>
>>
>>
>>amber8/linux redhat enterprise/dell pc
>>
>>
>>
>>Any thoughts, ideas or suggestions would be welcome.
>>
>>
>>
>>
>>
>>Dave Wells
>>
>>Imperial College London
>>
>>
>>
>
>
>
> 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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