[gmx-users] PME usage in 3.3 & g_energy: doubt ?

Luca Mollica mollica.luca at hsr.it
Tue Aug 1 17:52:17 CEST 2006

> First, with rlist = rvdw, you will not get long range Lennard Jones
> interactions. In fact I would recommend using a larger vdw cut-off, as
> 0.9 is very short. Are you sure you are using the same mdp file?

Yes it is .... and I have used the standard values suggested by GROMACS guide.
(3.2 and 3.3 as well, non bonded section, long range electrostatics interactions). This value is widely 
applied elsewhere in literature: but, ok, I can consider for the future the increase of rvdW values for 
improving calculations accuracy. Thank you.

> About the LR coulomb, it will only appear if you have rlist < rcoulomb.

Sure, I got it, standard issue ... that was the point: my doubt was about the difference between the two 
versions. Indeed, in GMX 3.2 I got the values even in PME, in 3.3 I do not have LR values and this was 
quite misleading.

> In that case the sphere between rlist and rcoulomb is frozen for the
> direct electrostatic interaction calculation during PME between two
> nlist updates (set by nlist = X).

Great .... ok, thanx for the answer: what I was supposing is now confirmed.
Now I feel more comfortable with this new GMX :)

Bye & thanx again


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