[gmx-users] Which coulmbtype?
r.k.badhan at stud.man.ac.uk
Mon Jan 5 20:50:01 CET 2004
Thank you for your response.
I have had a look at the g_mindist, and have found out that the
minimum distance is aprox 4.7nm.
When I come to paramatise this in the mdp file, should I use values
around this (i.e. 5 ) for rcoulomb/rvdw/rlist?
> 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.
> _____________ _______________________________________________________
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> | _ _ ___,| K. Anton Feenstra |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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