[gmx-users] PME question in GMX4.6.5
Tom
dnaafm at gmail.com
Tue Jan 13 06:17:39 CET 2015
Mark,
Thanks for the discussion!
Can you give me more detialed information?
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!
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)
*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?
If Coulomb (SR) with PME means the short-rang Coulombic within rcoulomb,
Coulomb (SR) with PME should very close to or equal to calculaton of the
same cutoff without PME.
I assume the Coulomb SR in PME is calculated by explicit pairwise
interaction like that of Cutoff
and Recip part uses Fourier Conversion.
I am really wondering if it is due to bugs of PME for this version: 4.6.5.
>> 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.
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
>
> >
>
>
>
More information about the gromacs.org_gmx-users
mailing list