[gmx-users] non-neutral system

Mon Nov 6 14:19:18 CET 2017

Hi Justin,

I have a system of 500 Argon fluid each given a charge +0.20 (vdW
cut-off=0.8 nm). So I expect the system to have total positive coulomb
potential (repulsion). Below are simualtion results of PME and cut-off:

PME coulomb results:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
LJ (SR)                    -2217.86       0.34    24.5444  -0.214063
(kJ/mol)
Coulomb (SR)           993.008       0.14    5.39276  -0.435068  (kJ/mol)
Coul. recip.               -11192.7       0.15    9.86392  -0.470106
(kJ/mol)
Potential                  -12417.5        0.6    33.2669   -1.11921
(kJ/mol)
Kinetic En.                 1224.39       0.44    44.2301   -2.79584
(kJ/mol)
Total Energy              -11193.1       0.94    54.8503   -3.91503
(kJ/mol)
Conserved En.          -17669        710    1446.14   -5008.59  (kJ/mol)
Temperature               196.74      0.071    7.10709  -0.449246  (K)

Cut-off coulomb results (0.8 nm):

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
LJ (SR)                    -2231.64       0.58    24.2735    2.05241
(kJ/mol)
Coulomb (SR)          94520.2        4.7    221.879   -9.05937  (kJ/mol)
Potential                   92288.5        4.5    217.531   -7.00686
(kJ/mol)
Kinetic En.                1257.31       0.43    45.3804   0.778738
(kJ/mol)
Total Energy              93545.9        4.1    221.992   -6.22759  (kJ/mol)
Conserved En.         518736      40000    81842.2     283452  (kJ/mol)
Temperature            197.031      0.069    7.29193   -0.125132  (K)

Best regards

On Mon, Nov 6, 2017 at 1:06 PM, João Henriques <joao.m.a.henriques at gmail.com
> wrote:

> Hi Johannes,
>
> I just meant that from a purely theoretical point of view, it needs to be
> neutral. This has to do with the convergence of the outer infinite series,
> as the paper Micholas linked clearly states. I sincerely hope I'm not
> botching this up, but this is the conclusion I've withdrawn from reading
> the literature. Now, if the software implementation contains some tricks to
> account for this, that I'm not familiar with and will therefore leave that
> discussion for someone else more acquainted with it.
>
> Cheers,
> J
>
>
>
> On Mon, Nov 6, 2017 at 12:03 PM, Hermann, Johannes <
> J.Hermann at lrz.tu-muenchen.de> wrote:
>
> > Hey Joao,
> >
> > are you sure? I think PME will introduce a neutralizing background
> charge?
> >
> > All the best
> >
> > Johannes
> >
> >
> >
> > On 06.11.2017 11:57, João Henriques wrote:
> >
> >> Hi,
> >>
> >> You shouldn't use PME without neutralizing the system's charge. It's a
> >> limitation of the Ewald summation. Take a look at the literature for
> >> further details.
> >>
> >> I don't know much about viscosity, so I'll leave that for someone else.
> >>
> >> Cheers,
> >> J
> >>
> >> On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh <fpoosaneh at gmail.com>
> >> wrote:
> >>
> >> Hi,
> >>>
> >>> I  have a system containing similar charged atoms. So the total charge
> is
> >>> not zero.
> >>>
> >>> Simulation results with cut-off coulomb seems reasonable,  but using
> PME
> >>> they are wrong (total columb potential is negative value which must be
> >>> positive). Any idea why?
> >>>
> >>> If I use counter-ions to neutralize the system, I am afraid the
> >>> properties
> >>> I am looking for (viscosity) will be influenced.
> >>>
> >>> Best regards
> >>> --
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> > --
> > ______________________________________
> > *Technische Universität München*
> > *Johannes Hermann, M.Sc.*
> > Lehrstuhl für Bioverfahrenstechnik
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