Re: [AMBER] About INP in case of MS=1

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 9 Oct 2013 09:53:43 -0700

The patch is already posted ... please follow the procedure to patch
all new patches make sure your test cases get passed, within
acceptable numerical accuracy.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Oct 8, 2013 at 11:03 PM, Hiromasa WATANABE
<hi-watanabe.hpc.co.jp> wrote:
> Dear Dr. Ray,
>
> Thank you very much for your rapid reply!
> I understood. I look forward to the patch.
>
> Thanks,
> WATANABE
>
>> Hiromasa,
>>
>> Yes, that's because the PB radius definition gets changed when INP=1
>> or when INP is the default value of 2.
>>
>> Wes will upload a patch to Amber12 to force the default radius
>> definition (radiopt) to remain as 0 whether INP=1 or INP=2. This has
>> been the case in the latest AmberTools release.
>>
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor,
>> Biochemistry, Molecular Biophysics, and
>> Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Wed, Oct 2, 2013 at 10:55 PM, Hiromasa WATANABE
>> <hi-watanabe.hpc.co.jp> wrote:
>>> Hi,
>>>
>>> About MM_PBSA in AMBER12, according to the manual,
>>> INP is a option for the case of MS=0, and INP has no influence in case of MS=1, I think.
>>>
>>> But, when MS=1,
>>> (1) INP=1
>>> (2) #INP=1
>>> these two computation produce different PBCAL.
>>>
>>> Does INP influence PB calculation in case of MS=1 ?
>>>
>>> How should I set INP when MS=1 ?
>>>
>>> --
>>> Hiromasa WATANABE
>>> Manager, Ph.D.
>>> HPC Dept., Technology Gr., HPC SYSTEMS Inc.
>>> Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
>>> Email: hi-watanabe.hpc.co.jp
>>> www.hpc.co.jp
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
> --
> Hiromasa WATANABE
> Manager, Ph.D.
> HPC Dept., Technology Gr., HPC SYSTEMS Inc.
> Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
> Email: hi-watanabe.hpc.co.jp
> www.hpc.co.jp
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Oct 09 2013 - 10:00:03 PDT