VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Aug 13 2021 - 08:48:24 CDT

How about writing to the developers of that plugin directly? If there is
no email there (there is certainly always one in the papers) opening an
issue on the GitHub repository would be the standard way to go.

Giacomo

On Fri, Aug 13, 2021 at 9:44 AM Ashar Malik <asharjm_at_gmail.com> wrote:

> I haven’t used this package.
>
> I would recommend using the methods listed by other developers that have
> developed plugins.
>
> For instance here is a package that requires setting up.
>
> https://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
>
>
> While this might not exactly contain the steps required for the package of
> your interest - it should give you a starting point.
>
> Otherwise write back and someone might be able to help.
>
> On Fri, 13 Aug 2021 at 8:59 PM, Prithwish Nandi <nandi.prithwish_at_gmail.com>
> wrote:
>
>> Hi Ashar,
>> Thanks for your reply.
>> Yes, I need this one.
>> So, this looks like that I need to
>>
>> In my case, I am using Big Sur version of Mac. How to set it up manually?
>> Not enough instructions are given in the GitHub link.
>> Regards,
>> Prithwish
>>
>>
>>
>> On Fri, Aug 13, 2021 at 1:21 PM Ashar Malik <asharjm_at_gmail.com> wrote:
>>
>>> Not all things come pre-packed with VMD.
>>> Some you have to manually set up.
>>>
>>> Is this what you are looking for?
>>>
>>> https://urldefense.com/v3/__https://github.com/limresgrp/FMAP_v1__;!!DZ3fjg!uB-qCzZvvEQPHtjNlAJpuCtg3V5sb4VquZJpPTd5GQRfWmdXv1GJXXk40EJnH_Xv0w$
>>> <https://urldefense.com/v3/__https://github.com/limresgrp/FMAP_v1__;!!DZ3fjg!rgIcKqszomS8clyBwanO3WucApargSWumvSyRtRfrzpZK7HJ3spNC5vRCpUs7O7vPw$>
>>>
>>>
>>> On Fri, 13 Aug 2021 at 7:43 PM, Prithwish Nandi <
>>> nandi.prithwish_at_gmail.com> wrote:
>>>
>>>> Hi,
>>>> I have seen a paper and youtube tutorial that describes how to model
>>>> funnel metadynamics using VMD.
>>>> Links are here: https://urldefense.com/v3/__https://www.nature.com/articles/s41596-020-0342-4.pdf__;!!DZ3fjg!uB-qCzZvvEQPHtjNlAJpuCtg3V5sb4VquZJpPTd5GQRfWmdXv1GJXXk40EIgNM2BAw$
>>>> <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-020-0342-4.pdf__;!!DZ3fjg!psj6AnfYyjXgd-a5dMzXZMS5zzSQv446klzpbw5u63OMxOJt13K6FpNxcl1mXBtaFQ$>
>>>>
>>>> https://urldefense.com/v3/__https://www.youtube.com/watch?v=usalRn6jNQo__;!!DZ3fjg!uB-qCzZvvEQPHtjNlAJpuCtg3V5sb4VquZJpPTd5GQRfWmdXv1GJXXk40EJ3ra0plg$
>>>> <https://urldefense.com/v3/__https://www.youtube.com/watch?v=usalRn6jNQo__;!!DZ3fjg!psj6AnfYyjXgd-a5dMzXZMS5zzSQv446klzpbw5u63OMxOJt13K6FpNxcl25KhER_Q$>
>>>>
>>>>
>>>> I am using VMD 1.9.4a in Mac.
>>>> I couldn't find any such plugin or the video/funnel.tcl script as shown
>>>> in this youtube video.
>>>> Has anyone of you ever used funnel metadynamics using VMD?
>>>>
>>>> Thanks,
>>>> Prithwish
>>>>
>>>>