[gmx-users] inter molecular distance restraints?

Mark Abraham mark.abraham at anu.edu.au
Tue Apr 11 16:39:00 CEST 2006

> Thank you for your 30 seconds.
> I guess what I was getting as, is there anything I should be aware of when
> applying distance restraints (known problems etc) that would have saved me
> making common mistakes.

Don't know, never done it.

> The gromacs manual is good, I would hesitate before saying wonderful....

I think it is an excellent *reference* manual, but it clearly not intended
as *tutorial* material. I find the former more valuable for a user
prepared to get their teeth into the problem they want to solve - learn
how and why things work and think about the properties of a good solution.
Frankly trying to do something as tricky as MD any other way is an
invitation to disaster, in my opinion. Some people want a tutorial-style
recipe to do something vanilla that doesn't require them to consider
whether they are doing something that will lead to a result that has
physical meaning. I'm happy ignoring these people unless they're wasting
my resources. I think that computational chemistry - even including ab
initio quantum chemistry - isn't the kind of thing you can approach with
the same mentality with which people approach mainstream shrink-wrap
commercial software. In a way, then, documentation that requires the user
engage in thinking in order to develop a successful outcome is actually


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