Samuel Silva Pita wrote:
Hi, GMXers,
i've some doubts about the use of GMX and implicit solvent models.
I have an huge system ( moreless 10 000 protein atoms) and trying to do MD
using explicit solvents but my computer limitations doesn't work very well.
1) someone could help me giving some light in how can i simulate my system in
vacuum? I tried and my protein colapses using PME and GMX FF number 4 in
GMX3.2.1;
Find a force field parameterized for vacuum simulations, or just use a
random number generator.
2) and so, if someone have tried to incorporate implicit solvents in
simulations like GB, SASA, or others . This would be useful for me if give me
some instructions.
sincerely,
Not in GROMACS. Try AMBER, or doubtless others.
Mark
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