VMD-L Mailing List

From: A. M.M (alaa.murar_at_gmail.com)
Date: Wed Apr 11 2018 - 11:37:01 CDT

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
>>>
>>
>>
>