[gmx-users] supervised MD in Gromacs?

João M. Damas jmdamas at itqb.unl.pt
Tue Dec 8 14:46:42 CET 2015

Dear Albert,

Unfortunately, the methods section of some papers does not reflect every
detail of what was done to achieve the results. In the particular case of
computational papers, this means the use of scripting (or even hacking) to
assist a more wide-spread code (like GROMACS). That being said, I do not
know what was done in those papers.

I have not read the papers, but these "supervised" techniques seem fairly
similar to the milestoning ones. Maybe find an alternative there?


On Tue, Dec 8, 2015 at 1:31 PM, Albert <mailmd2011 at gmail.com> wrote:

> Thanks a lot for comments.
> May I ask what kind of Gromacs utilities should be involved? For sure,
> Gromacs definitely could do this so called "supervised MD", since one of
> the work was claimed done in Gromacs.....
> Albert
> On 12/08/2015 01:45 PM, Vitaly V. Chaban wrote:
>> The only thing you need is to arrange the existing gromacs utilities into
>> a
>> script. Python, Perl, Bash languages do this very well.
>> P.S. It is not very honest of the algorithm authors to call it
>> *unconstrained*  while they simply disregard motions that they do not
>> like.
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João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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