Luca Mollica wrote:
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.
DO NOT use rlist < rcoulomb with PME though! You will have a weird mix
where forces between particles at distance smaller than rcoulomb and
larger than rlist are update only every nstlist steps, and distances
smallar than rlist *and* distances larger than rcoulomb are updated
every step.
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
Luca
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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