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

[Giovana Bergamini]

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?

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

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Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul