[gmx-users] Which coulmbtype?

[Raj Badhan]

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?
Many thanks

> 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 |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.


Raj Badhan
Postgraduate researcher
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.