VMD-L Mailing List

From: Prithwish Nandi (nandi.prithwish_at_gmail.com)
Date: Fri Aug 13 2021 - 08:27:08 CDT

Thanks Asar for the hints.
I'll check it out.
Regards,
Prithwish

On Fri, Aug 13, 2021 at 2:06 PM 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!oS-09EJgKnaW-Ep1gdAqwBehY_bbSLD_2d9c4FIUI0h2GrC1R-IUYvQuH-ISC3VFoQ$
>>>
>>>
>>> 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!oS-09EJgKnaW-Ep1gdAqwBehY_bbSLD_2d9c4FIUI0h2GrC1R-IUYvQuH-L0q1CM3g$
>>>> <https://urldefense.com/v3/__https://www.nature.com/articles/s41596-020-0342-4.pdf__;!!DZ3fjg!psj6AnfYyjXgd-a5dMzXZMS5zzSQv446klzpbw5u63OMxOJt13K6FpNxcl1mXBtaFQ$>
>>>>
>>>> https://urldefense.com/v3/__https://www.youtube.com/watch?v=usalRn6jNQo__;!!DZ3fjg!oS-09EJgKnaW-Ep1gdAqwBehY_bbSLD_2d9c4FIUI0h2GrC1R-IUYvQuH-JrqGD6Pg$
>>>> <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
>>>>
>>>>