And at what time point does it explode? What minimization, equilibration steps did you use?
On 13 May 2010 18:53, Giovana Bergamini <[email protected]> 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 > > -------------------------------------------------------------------- > Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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