there is info on the archive about this for the mdcrd file, which is
handled the same way.
http://archive.ambermd.org/200912/0221.html
On Tue, Jun 28, 2011 at 7:01 AM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Professor Simmerling,
>
> Thank you for your comment.
>
> The difference between them is around 1% at most.
>
> For a system with c.a. 39000 atoms at 300 [K],
>
> Kinetic energy in mdout: 24065.6974
> Kinetic energy calculated: 24357.5391
>
>
> I am most grateful if you tell me the time step
> when mdout and mdvel are written down.
>
> Yours sincerely,
>
> Ikuo Kurisaki
>
>
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: Tuesday, June 28, 2011 7:48 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Kinetic energy in mdout file is not identical to that
> calculated from mdvel file.
>
> How much different? The mdvel and mdout are not written at the same time
> step.
> On Jun 28, 2011 4:22 AM, "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp>
> wrote:
>> Dear Amber developers and users,
>>
>>
>>
>> Thank you for kind support and useful comments every time.
>>
>>
>>
>> Now, I need to compare solute temperature and solvent temperature.
>>
>>
>>
>> So first, I calculated kinetic energy of all system using a mdvel file,
>>
>> But I found the kinetic energy in mdout was not identical to that derived
> my
>> calculation.
>>
>>
>>
>> I calculated kinetic energy by following two way:
>>
>> (1) Microsoft excel
>>
>> (2) In house program with python.
>>
>> The values obtained from (1) and (2) were just matched but different from
>> that in mdout.
>>
>>
>>
>> Is this difference arisen from computational feature of AMBER?
>>
>> Or just bug or my mistake?
>>
>>
>>
>> I am most grateful if you experienced similar cases and give me some
>> advices.
>>
>>
>>
>> Thank you for your kind support.
>>
>>
>>
>> Ikuo Kurisaki
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jun 28 2011 - 12:00:05 PDT
