AMBER Archive (2005)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Mar 22 2005 - 16:59:00 CST

Another simple workaround is to turn off the search for water molecules
by setting jfastw = 4.

Best,
Ray

Ray Luo wrote:

> 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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