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

[Oliver Grant]

And at what time point does it explode? What minimization, equilibration
steps did you use?

On 13 May 2010 18:53, Giovana Bergamini <gioberga at cbiot.ufrgs.br> 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?
>
> 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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