[gmx-users] Structure optimization failure

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 19:59:43 CEST 2012

On 6/29/12 11:10 AM, massimo sandal wrote:
> On 29 Jun 2012 15:09, "Justin A. Lemkul" <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>  >
>  >
>  >
>  > On 6/29/12 9:04 AM, massimo sandal wrote:
>  >>
>  >>
>  >> On 29 Jun 2012 14:08, "Justin A. Lemkul" <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>  >>
>  >>  >
>  >>  > The settings in my tutorial are for use with OPLS-AA and are thus not
>  >> suitable for a simulation with CHARMM.  Cutoffs and other aspects will be
> different.
>  >>
>  >> This is interesting. In general, where can you find optimal mdp settings for
>  >> each force field?
>  >>
>  >
>  > By reading the primary literature for how each force field was derived.  The
> parameters are only guaranteed to work within the context of correct cutoffs,
> electrostatic schemes, neighborlist update interval, water model used, etc. Some
> older force fields have been demonstrated to work well with PME even if
> originally derived with RF or some other method, but generally the other
> settings must adhere to the original parameterization.  Some force fields can be
> very sensitive to these incorrect settings.
>  >
>  >
> Yes, I know, but I hoped someone could have put a table online or wrote a book
> chapter somewhere about this.
> 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.

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

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.

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.

Just my $0.02.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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