[gmx-users] PME usage in 3.3 & g_energy: doubt ?
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 1 17:44:52 CEST 2006
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
> (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
>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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