[gmx-users] supervised MD in Gromacs?

[João Henriques]

Albert, we need to get some things straight:

1) Please notice that your affirmation about failing to report a method in
a paper published through a peer-reviwed journal is quite serious, and can
have consequences.
2) The authors are entitled to comercialize their intellectual property.
It's not for us to judge.
3) The algorithm is public. Their code is not. Then, like I said, code your
own version. There's literally nothing hindering you from doing it.

Best regards,
João

On Tue, Dec 8, 2015 at 2:54 PM, Albert <mailmd2011 at gmail.com> wrote:

> I contacted the second author, and he told me that he also used
> "supervised MD" although he didn't mention it explicitly in the paper.
>
> Meanwhile, I found that the original author probably set up a company
> based on this method:
>
>
> https://www.acellera.com/supervised-molecular-dynamics-sumd-helpful-tool-depict-gpcr-ligand-recognition-pathway-nanosecond-time-scale/
>
> probably he is going to make money with it.....
>
> regards
>
>
>
>
> On 12/08/2015 02:50 PM, João Henriques wrote:
>
>> In addition to what Justin said, please notice that the reference by
>> Wittmann et al does not use SuMD. From what I read it uses standard MD
>> simulations. The other reference, where SuMD is actually presented, gives
>> all necessary information to produce your own version of it, since the
>> authors are unwilling to share their scripts (according to you).
>>
>> What GROMACS tools need to be involved? That is for you to investigate.
>> Study their method and assess what program needs to be called at which
>> step. You'll also need to code a wrapper or a script to automate the
>> algorithm.
>>
>> In sum, unfortunately there's no take away available, you need to prepare
>> and cook the meal yourself.
>>
>> /J
>>
>
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