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:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
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
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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