[gmx-users] supervised MD in Gromacs?

[João Henriques]

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


On Tue, Dec 8, 2015 at 2:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/8/15 8:29 AM, Albert wrote:
>
>> That's a little bit strange.
>>
>> As in paper:
>> Binding pathway of histamine to the hH4R, observed by unconstrained
>> molecular
>> dynamics
>> http://www.sciencedirect.com/science/article/pii/S0960894X15000645
>>
>>
>> The author claimed that all the simulation was done in Gromacs
>>
>> I contacted them several times, they never reply when I request to share
>> their
>> script/configuration file/MD details. ....
>>
>>
> That may be telling.  Also note that their methods are also questionable
> (even getting terminology like "constraints" wrong, using PRODRG for the
> ligand - yikes!) so tread carefully.  I haven't looked at the papers
> closely so I will not comment much further.
>
> It is unfortunately commonplace when writing methods to simply say the
> simulations were performed with GROMACS, but conveniently leave out lots of
> technical details like additional scripts, external wrappers, programs,
> etc. The MD engine may have been GROMACS, but it was either (1) modified
> in-house or (2) called as part of some larger workflow using scripting and
> other utilities.
>
> -Justin
>
> regards
>>
>> Albert
>>
>>
>> On 12/08/2015 12:04 PM, João Henriques wrote:
>>
>>> _*As far as I know*_, the SuMD algorithm is not implemented in GROMACS.
>>> _*I
>>> only took a peek at the respective reference*_, but it seems rather
>>> cryptic in
>>> the sense that no indication appears to be given as to which MD software
>>> this
>>> was implemented on, if it's available, etc.
>>>
>>> I also _*took a peek*_ at the other paper, and it seems like they just
>>> run
>>> simple, standard unconstrained MD simulations. Nothing fancy here.
>>>
>>> NOTE: The underlined bold text is on purpose to let anyone know that I
>>> may be
>>> wrong, because I didn't dwell on the subject.
>>>
>>> /J
>>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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>
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