[gmx-users] Which coulmbtype?

[Anton Feenstra]

Raj Badhan wrote:

> Dear All,
> I'm a little confused as to which coulmbtype to use in my md 
> simulations.
> 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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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