[gmx-users] Which coulmbtype?
feenstra at chem.vu.nl
Mon Jan 5 09:35:04 CET 2004
Raj Badhan wrote:
> Dear All,
> I'm a little confused as to which coulmbtype to use in my md
> From what I understand, PME generally is the method of choice, if
> somewhat slower then cutoff. However, with my simulations I
> always seem to get the box exploding or nan errors during
> simulations with ATP in a water box. I've checked my system and
> there are no bad contacts.
> Can anyone suggest any suitable parameters that work for them
> when using ligands such as ATP?
Do you have enough water around your ATP, or in other words is your
box large enough? You can use g_mindist -pi to chech the 'minimum
periodic distance' of ATP to its periodic images during the simulation. That should be
at least 1 nm, but for PME maybe one would want that larger.
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| _ _ ___,| K. Anton Feenstra |
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