[gmx-users] Simulation explodes (protein-ligand-protein)

Justin A. Lemkul jalemkul at vt.edu
Thu May 13 23:24:22 CEST 2010

Giovana Bergamini wrote:
> Hi!
> We have a problem with a protein-ligand-protein simulation. It is a somewhat
> large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
> that requires a larger box for proper simulation.
> We used exclusions (especifically for the problematic atoms) and restrictions
> (tested values of 5000, 2000, 1000 - for backbone and for monosaccharides),
> both combined and individually, and when they were kept for the entire
> simulation, it went just fine. But when these restrictions and exclusions were
> removed, the glycan portion, that isn’t connected to any of the proteins
> “explodes”.
> Any suggestions?

It sounds like the exclusions and restraints are acting as artificial 
stabilizing factors, leading to the conclusion that the underlying system is 
unstable.  Exclusions may or may not be appropriate - some force fields utilize 
intramolecular exclusions.  If you're excluding energy terms between molecules, 
however, that's not appropriate.

You haven't provided much information about how the system was built, what force 
field you're using, the success of energy minimization, .mdp parameters, etc. 
All of that (and possibly more) may be necessary to diagnose what's going on, 
otherwise, the standard reading applies:



> Thank you in advance,
> Giovana Bergamini
> Faculdade de Farmácia
> Grupo de Bioinformatica Estrutural
> Universidade Federal do Rio Grande do Sul
> Av. Bento Gonçalves, 9500
> Prédio 43431, sala 202
> CEP 91500-970, CP 15005, Porto Alegre, RS, Brazil
> tel.: +55 51 3308 7770
> http://www.cbiot. ufrgs.br/ bioinfo
> --------------------------------------------------------------------
> Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul


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


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