[gmx-developers] minimization limitations

Leontyev Igor ileontyev at ucdavis.edu
Tue Jun 2 04:05:49 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. 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 ?

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.

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