[gmx-users] Structure optimization failure

ms devicerandom at gmail.com
Sat Jun 30 14:18:12 CEST 2012

On 29/06/12 19:59, Justin A. Lemkul wrote:

>> Wouldn't it be nice to create a table of "standard settings" for each
>> forcefield
>> in the gmx documentation (with lit references of course)?
> Well, anyone is welcome to submit anything they feel would be useful... ;)
> I have considered this in the past, but have rejected the thought every
> time it comes to mind. It would be nice if there was a central
> repository of such parameters, but then likely a simulation becomes "do
> this, not that" with no required thought from the end user.
> If you make
> simulations a black box, everyone expects them to automatically work
> without fail.

Which should be what it has to be in an ideal world :)

Apart from that, it wouldn't mean to make them a black box -quite the 
opposite. Giving parameters *with* an explanation of them, literature 
quotes etc. would give tremendous insight to lots of people that often 
just use "the lab's standard .mdp" and tweak it.

This doesn't mean everyone would expect them to work without fail, it 
would give however a good starting point.

> The other objection I have always had is the continual improvement of
> the field. If Gromacs puts out an "official" or "standard" list of what
> to do, it is always subject to change and then becomes incumbent upon a
> Gromacs contributor to verify its accuracy frequently. My personal fear
> is that this becomes an untenable task.

Isn't that however the point of a scientific community -sharing and 
updating knowledge? We use to rely on papers, but that's far more 
inefficient than having a centralized repo where we can share and 
discuss informations.

> Then in the case of an error,
> someone's whole Ph.D. could go out the window...

I suspect without this even more Ph.D's get wasted -because they don't 
really know what to do and just crank things together without really 
getting it. Not all of us have received proper education on MD (I didn't 
for example -I had to learn everything by myself and I am a total newbie 
even after a couple years) I mean, at least it gives a good starting 
point for people.

> In the end, I think it's always safe to ask the user to do a bit of
> legwork to understand the force field he or she wishes to use. The
> knowledge gained from an hour of reading will save a lot of potential
> headaches.

Sure, and in fact I would expect such a page etc. to *start* with 
literature references and even directly quoting papers when explaining 
why certain params and not others.

> I would reject any attempt to include such information in the manual
> (lest its settings become "official"), but if someone wants to put up a
> wiki page on the website with clear warnings and disclaimers, they are
> welcome to do so.

I am probably the least qualified person to do so, but I'd enjoy to 


> Just my $0.02.
> -Justin

Massimo Sandal, Ph.D.

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