[gmx-users] Re PME question in GMX4.6.5
Tom
dnaafm at gmail.com
Thu Jan 15 01:25:14 CET 2015
Mark,
Thanks for your reply!
I actually found this disscussion about PME, which might be from you?
https://groups.google.com/forum/#!topic/archive-gmx-users/VmK7H5vF9cY
you were saying:"The total energy for that interaction is distributed over
the Coul-SR and *Coul. recip terms (which is how PME works...), which you
will note is approximately equal to Coul-SR for coulombtype cut-off*."
That is why I run these test runs and found that Coul.recip from PME has big
difference from Coul-SR from coulombytpe cut-off.
Anyway, i will double check the menual and the source code as well your
paper.
Thomas
> ------------------------------
>
> Message: 3
> Date: Tue, 13 Jan 2015 07:32:25 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Cc: Discussion list for GROMACS users
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] PME question in GMX4.6.5
> Message-ID:
> <CAMNuMAT7hyKHCLAqVtFOz4v7N9qzpU-MkyFY2=
> HquJN6RTbLdg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Tue, Jan 13, 2015 at 6:17 AM, Tom <dnaafm at gmail.com> wrote:
>
> > Mark,
> >
> > Thanks for the discussion!
> > Can you give me more detialed information?
> >
>
> Please start by reading the manual sections (4.8 and 3.17.5).
>
>
> > Yes, I do need a higher speed so I choose the option to periodic
> > electrostatic sum into two terms: SR & recip.
> >
> > Is there other more decent way to do it? Thanks!
> >
>
> No, but you can do PME differently, and perhaps better, for your simulation
> system and your hardware. Shameless self-plug:
> http://dx.doi.org/10.1002/jcc.21773, but mdrun does some of this for you,
> these days.
>
> This was what I used for PME
> > -----------------------------
> > nstlist = 10
> > ns_type = grid
> > rlist = 1.2
> > rcoulomb = 1.2
> > rvdw = 1.2
> > ; Electrostatics
> > coulombtype = PME ; Particle Mesh Ewald for long-range
> > electrostatics
> > ewald_geometry = 3dc
> > pme_order = 4 ; cubic interpolation
> > fourierspacing = 0.12 ; grid spacing for FFT
> > -------------------------------
> >
> > I gave a test by using different
> > *Case 1) PME: **coulombtype = PME**; **rlist =1.2; rcoulomb=1.2;
> > rvdw=1.2*
> > Coulomb (SR) (= 3.88670e+05) *<* Coul. recip.(3.09251e+06)
> > *Case 2) PME: **coulombtype = PME**; **rlist =1.2; rcoulomb=1.2;
> > rvdw=1.2*
> > Coulomb (SR) (= 1.00323e+06) *<* Coul. recip.(2.47795e+06)
> >
>
> What's different between these two cases? (But doesn't matter, the real
> issue is below)
>
>
> > *Case 3) No PME:* *coulombtype = cutoff; rlist =1.2; rcoulomb=1.2;
> > rvdw=1.2*
> > Coulomb (SR) = 3.33299e+06
> > *Case 4) NO PME: coulombtype = PME**; rlist =1.8; rcoulomb=1.8;
> > rvdw=1.8*
> > Coulomb (SR) = 3.99204e+06
> >
> > Even for same rlist, rcoulomb and rvdw, the value by using the cutoff of
> > 1. 2 (Coulomb (SR) =3.33299e+06) (see Case 1) is much larger than the
> value
> > of Coulomb (SR) (= 3.88670e+05)
> > by using PME with *rlist =1.2; rcoulomb=1.2; rvdw=1.2* (See Case 3).
> > Why there is such big difference?
> >
>
> None of the above are meaningful to compare. By using plain cutoff, you are
> neglecting an extremely large number of interactions, so it is not
> surprising any numbers are different. By changing the size of the
> short-range region, you are shifting computation from one part to another,
> so it is not surprising that numbers are different.
>
> If Coulomb (SR) with PME means the short-rang Coulombic within rcoulomb,
> >
>
> But it isn't. See equation 4.158 of manual.
>
>
> > Coulomb (SR) with PME should very close to or equal to calculaton of the
> > same cutoff without PME.
> >
>
> Nope. The short-ranged part is modified, and the long-range part corrects
> for the short-range modification and the neglected long-range part of the
> unmodified potential. People often speak loosely about this, unfortunately.
>
> I assume the Coulomb SR in PME is calculated by explicit pairwise
> > interaction like that of Cutoff
> > and Recip part uses Fourier Conversion.
> >
>
> Yes, but the SR part is not 1/r any more.
>
>
> > I am really wondering if it is due to bugs of PME for this version:
> 4.6.5.
> >
>
> Not on the available evidence.
>
> >> I'll bet lunch that the input was not actually from the PME run ;-)
> > We do need to use g_energy to output the total Coulombic interactions
> > between certains objects
> > in the system. Now the recip. part is much larger than SR part but the
> > recip. part can not be reported
> > by g_energy.
> >
>
> g_energy will report the reciprocal-space energy if the input file you gave
> it had such a component. mdrun with PME wrote such a file. Your observation
> is most consistent with not using the file you think you are using.
>
> If you're wanting the reciprocal space component to be broken down by
> energy group, then that's not available. Someone on this list once observed
> that you can use mdrun -rerun creatively with various components charges
> zeroed out in order to compute that break down. Whether that then
> correlates with anything useful is... your problem.
>
> Mark
>
> Can you let us know if there is any wrong in our inputs for PME?
> >
> > Thanks!
> >
> > Tom
> >
> >
> >
> >> Message: 5
> >> Date: Mon, 12 Jan 2015 18:44:56 +0100
> >> From: Mark Abraham <mark.j.abraham at gmail.com>
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Subject: Re: [gmx-users] PME question in GMX4.6.5
> >> Message-ID:
> >> <
> >> CAMNuMAREBb8Ny5KfOudKUX-gvwQHhOX6MRphDUfPkTtR5bHPag at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> On Sat, Jan 10, 2015 at 5:58 PM, Tom <dnaafm at gmail.com> wrote:
> >>
> >> > Dear GMX and PEM experts,
> >> >
> >> > I am using gromacs 4.6.5. My system is neutral charge (net charge=0).
> >> > I used PME with the following options:
> >> > -------------
> >> > ; Electrostatics
> >> > coulombtype = PME ; Particle Mesh Ewald for long-range
> >> > electrostatics
> >> > ewald_geometry = 3dc
> >> > pme_order = 4 ; cubic interpolation
> >> > fourierspacing = 0.12 ; grid spacing for FFT
> >> > --------------
> >> >
> >> > I noticed that for my system *with PME calculation *that value of
> >> *Coulomb
> >> > (SR) is much*
> >> > *larger than Coul. recip*
> >> > Coulomb (SR) (= 3.88670e+05) < Coul. recip.(3.09251e+06)
> >> >
> >> > Do you think if it is possible to have such as huge tail effects of
> >> > Coulombic interactions?
> >> >
> >>
> >> You chose a set of parameters that split the computation of the full
> >> periodic electrostatic sum into two terms whose sum approximates the
> full
> >> one while hopefully being cheaper to compute. The relative magnitude of
> >> the
> >> energies doesn't mean much of anything...
> >>
> >> (My systems consist of a neutral SAMs surface and water)
> >> > Another problem is that g_energy of GMX4.6.5 only reports the value of
> >> > Coulomb (SR) and
> >> > does not report Coul. recip.
> >> >
> >>
> >> I'll bet lunch that the input was not actually from the PME run ;-)
> >>
> >> I also used simple *cutoff* to calcualte coulombic:
> >> > Coulomb (SR) = 3.99204e+06 *is the very close to the PME *calculation
> >> of
> >> > the total of Coulomb (SR) + Coul. recip.
> >> >
> >>
> >> Great, but this is a totally different (and terrible) approximation.
> >>
> >> Mark
> >>
> >>
> >> > Thanks a lot for your help!
> >> >
> >> > Thomas
> >>
> >> >
> >>
> >>
> >>
> >
>
>
>
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