[gmx-developers] Re: minimization limitations

Igor Leontyev ileontyev at ucdavis.edu
Tue Jun 2 11:00:44 CEST 2009

>> The bug with minimization seems to be fixed now, see
>> http://bugzilla.gromacs.org/show_bug.cgi?id=332. Thank you Berk. With
>> corrected sources "csettle.c" and "minimize.c" the new 4.0.5 version is
>> able
>> to minimize my MD system at least on the same level as it was possible in
>> 3.3.1 version.
>> At this point I would like to mention 2 more limitation of the
>> minimization
>> procedure implemented in gromacs.
>> 1) Since a dynamics of complex biological system depends on quality of
>> the
>> minimized structure, a fine minimization is very important.

>Generally, I would think not. The process of assigning atomic velocities
>randomly sampled from a suitable distribution "undoes" the finest part of
>the minimization. Then one needs to equilibrate, possibly under position
>restraints, which also leaves the structure perturbed from the input
>structure, but hopefully still in the same local minimum region. See also
>comments in manual section 3.10.

It's true if the finer energy minimization do not exceed ~(kT) relatively to
the "steep" method for each site of the complex protein+solvent system. But
it's hard to ensure for each site. Moreover, there are applications of the
minimized structures other than MD simulations, in which there is no atomic
velocities.  For example, continuum electrostatic pKa calculation needs as
an input the protein structure with optimized hydrogen positions.

>> Is there way in
>> gmx to reFINE minimization of the system with many different constraints
>> ?

> See manual. You can make the waters flexible, or use L-BFGS for
> single-processor minimization.

I have been tried to use all described in manual options but result was not
Flexible water model does not solve the problem for my system with
constrained hbonds and other constraints or frozen atoms. L-bfgs results to
the structure where some hydrogens are locked in the local minimum which is
far away from the global one. I just ran l-bfgs minimization starting from
the minimized by the "steep" method configuration and found that one of
van-der-Waals-less hydrogen atoms in the final structure is transferred to
 the vicinity (~0.1A) of some negative nitrogen but far away (~3.0A) from
its heavy atom . This local minimum is far away from global one due to huge
bond-stretching penalty of the h-bond.

>> 2) After steepest descent minimization  of the protein+solvent system,
>> the
>> positions of the frozen TIP3P water molecules are slightly shifted (~0.3
>> A).
>> The shift of frozen molecules is really bothering.

> Are you centering the structures on the same frozen atom? Otherwise you
> may just be seeing a shift of reference frame.

"Frozen" (by freezegrps) means in respect to the initial configuration,
isn't it?

More information about the gromacs.org_gmx-developers mailing list