[gmx-users] D-Ala topology for OPLSAA

[Anton Feenstra]

Attila Borics wrote:
> Erik,
> 
> Yes, I expected the same, but when I try to run pos.res. dynamics it
> keeps crashing after 40-500 2fs steps. I suspected my tip4p water box
> too, that it's not well equilibrated, but that just worked fine in my
> previous simulation....that shouldn't be the problem

Can you run it stable without posres, or can you do an em?

Have you looked at energies, or residue coordinates that go wild?

Is 2fs a good timestep with explicit hydrogens? You could use the
-dummy hydrogens option of pdb2gmx to 'freeze' the internal
degrees of freedom of the hydrogens (see J. Comput Chem 20 789-798,
or the Gromacs manual for method details).


-- 
Groetjes,

Anton
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|        | Anton Feenstra                                            |
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