[gmx-users] Detail of MSD Calculation Method

[behnam ghalami]

 Thank you for the response

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On Sun, Jul 1, 2018 at 11:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/1/18 2:44 PM, behnam ghalami wrote:
>
>> Many thanks for your help
>> How I can gain the source code?
>>
>
> http://manual.gromacs.org/documentation/2018.2/download.html
>
> -Justin
>
>
> On Sun, Jul 1, 2018, 22:58 Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>>
>>> Unfortunately there is only the gmx help output, and the source code of
>>> the
>>> tool itself.
>>>
>>> Mark
>>>
>>> On Sun, Jul 1, 2018, 16:28 behnam ghalami <ghalamichoobar at gmail.com>
>>> wrote:
>>>
>>>   Dear Gromacs Users
>>>>
>>>> I would like to compute diffusion coefficient using Homemade code by
>>>>
>>> below
>>>
>>>> equation;
>>>> However my obtained results differ from that of gmx msd and there is 5
>>>> percent difference of msdanalyzer package which I found it in internet.
>>>> Where I can find a comprehensive detail about numerical procedure
>>>>
>>> employed
>>>
>>>> in Gromacs. Any information you can provide me would be greatly
>>>> appreciated.
>>>>
>>>> Regards
>>>>
>>>> <
>>>>
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> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
Behnam Ghalami Choobar
PhD Candidate in Chemical Engineering
Amirkabir University of Technology, Tehran-Iran