[gmx-developers] minimization limitations

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jun 2 05:58:47 CEST 2009

Leontyev Igor wrote:
> 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.

> For the fine
> minimization the conjugated gradient (cg) method should be used rather than
> the steepest descent. However, the "cg" minimization fails for my system,
> presumably, due to bond-constrains needed for TIP3P water. 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.

> 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.


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