[gmx-users] supervised MD in Gromacs?

Justin Lemkul jalemkul at vt.edu
Tue Dec 8 14:42:32 CET 2015

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.


> 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


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