VMD-L Mailing List

From: A. M.M (alaa.murar_at_gmail.com)
Date: Wed Apr 11 2018 - 11:37:52 CDT

بسم الله الرحمن الرحيم

Sorry, the installation methods link:
https://gist.github.com/tonigi/a9cfaf7642a7fbc13293

Thanks

On Wed, Apr 11, 2018 at 7:37 PM, A. M.M <alaa.murar_at_gmail.com> wrote:

> بسم الله الرحمن الرحيم
>
> Hello,
>
> follow the following link (Method 3 if you have VMD 1.9.2 or higher) to
> add this plugin to VMD and instead of the code used in the link for (method
> 3) use this code with replacing "*/WHERE/YOU/EXTRACTED/THE/TOOL*" to your
> plugin path:
>
> lappend auto_path */WHERE/YOU/EXTRACTED/THE/TOOL*
> vmd_install_extension diffusion_coefficient_gui \
> diffusion_coefficient_gui::diffusion_coefficient_tk \
> "Analysis/Diffusion Coefficient Tool"
> menu main on
>
> Another thing, I advise you to look at the document/figure that comes with
> this plugin to know how it calculates the MSD and D_coeff clearly.
>
> Thanks
>
>
> On Wed, Apr 11, 2018 at 7:27 PM, A. M.M <alaa.murar_at_gmail.com> wrote:
>
>> بسم الله الرحمن الرحيم
>>
>> Hello,
>>
>> This is the MSD and D_coeff plugin for VMD link:
>> https://github.com/tonigi/vmd_diffusion_coefficient
>>
>> Thanks
>>
>>
>> On Wed, Apr 11, 2018 at 6:52 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>> wrote:
>>
>>> Hi Jeams,
>>>
>>> There is some plugin in VMD for calculating diffusion co-efficient and
>>> MSD. You can add those plugin to your VMD.
>>> You can check in the link below-
>>> https://sourceforge.net/p/membplugin/wiki/Home/
>>>
>>> Thanks.
>>> Rabeta
>>>
>>>
>>> On Wed, Apr 11, 2018 at 8:14 AM, Jeams Anderson <anddersonnyc_at_gmail.com>
>>> wrote:
>>>
>>>> Dear all
>>>>
>>>> I am wondering is it possible to calculate MSD or diffusion coefficient
>>>> in VMD??
>>>>
>>>> Any suggestion will be very helpful
>>>>
>>>> Thanks in advance
>>>>
>>>> Regard
>>>>
>>>> Jeams
>>>>
>>>
>>>
>>
>