Dear Prof. Simmerling,
Thank you for your kind support.
Sincerely yours,
Ikuo Kurisaki
-----Original Message-----
From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
Sent: Wednesday, June 29, 2011 3:50 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Kinetic energy in mdout file is not identical to that
calculated from mdvel file.
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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 30 2011 - 20:30:03 PDT
