[gmx-users] net charge correction
Mark Abraham
mark.j.abraham at gmail.com
Wed Jun 15 15:13:45 CEST 2016
Hi,
On Wed, Jun 15, 2016 at 12:05 PM Michael Brunsteiner <
michael.brunsteiner at tugraz.at> wrote:
>
> Hi,
>
> In an attempt to understand how gromacs deals with electrostatic
> (long range) interactions in systems with a net-charge i made couple
> of simple model systems....
> Calculating the energy of a system with a SINGLE charge on only ONE atom
> in a periodic system with PME I get:
>
> gmx energy -f one.edr
> Coulomb (SR) -204.026 -- 0 0 (kJ/mol)
> Coul. recip. 207.208 -- 0 0 (kJ/mol)
>
> (sys specs and input files below)
>
> Since I use PME i get as expected a non-zero "Coul. recip." while
> Coulomb(SR)=-204.026 is the self energy (V_0 in eqn. 4.163 of the manual)
> what i am missing is a correction term for systems with a net-charge
> that is typically
> proportional to the square of the net-charge divided by the volume. Is this
> term included in Coul.recip
Yes. See function ewald_charge_correction in the source code.
> or do i have to calculate it myself and add
> it explicitly?
>
> Is there a way to ask gromacs to explicitly provide:
> 1) the individual terms in eqn. 4.161-4.163 of th3e manual
> 2) the dipole correction (epsilon-surface>0)
> 3) the net-charge correction
>
> ?
>
No, these are all dumped into Coul. recip. See code in
src/gromacs/ewald/long-range-correction.cpp
Mark
> thanks for any help!
> Michael
>
>
>
> ==================================================
> system:
> gromacs 5.1.2 on ubuntu 14.04, 64 bit
> same result with both single and double prec.
>
> ==================================================
> mdp file:
>
> integrator = md
> nsteps = 0
> comm-grps = System
> ;
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 0
> nstenergy = 1
> ;
> nstlist = 1
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> cutoff-scheme = Verlet
> ;
> coulombtype = PME
> rcoulomb = 1.2
> vdw_type = cut-off
> rvdw = 1.2
> ;
> constraints = none
> continuation = yes
>
> ==================================================
> top file:
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5 0.8333
>
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> o o 10.00000 -1.00000 A 0.000000 0.000000
> c c 10.00000 1.00000 A 0.000000 0.000000
> n n 10.00000 0.00000 A 0.000000 0.000000
>
>
> [ moleculetype ]
> ;name nrexcl
> o 3
>
> [ atoms ]
> ; nr type resi res atom cgnr charge mass
> 1 o 1 MM1 O 1 -1.00000 10.0000
>
>
> [ moleculetype ]
> ;name nrexcl
> c 3
>
> [ atoms ]
> ; nr type resi res atom cgnr charge mass
> 1 c 1 MP1 C 1 1.00000 10.0000
>
>
>
> [ moleculetype ]
> ;name nrexcl
> n 3
>
> [ atoms ]
> ; nr type resi res atom cgnr charge mass
> 1 n 1 NEU N 1 0.00000 10.0000
>
>
> [ system ]
> system
>
> [ molecules ]
> n 1
> n 1
> n 1
> n 1
> n 1
> n 1
> n 1
> c 1
>
>
> ==================================================
> input structure:
>
> CRYST1 41.461 66.148 200.000 90.00 90.00 90.00 P1
> ATOM 1 N NEU 1 20.000 30.000 100.000 0.00 0.00
> ATOM 2 N NEU 2 20.000 33.000 100.000 0.00 0.00
> ATOM 3 N NEU 3 23.000 33.000 100.000 0.00 0.00
> ATOM 4 N NEU 4 23.000 30.000 100.000 0.00 0.00
> ATOM 5 N NEU 5 20.000 30.000 103.000 0.00 0.00
> ATOM 6 N NEU 6 20.000 33.000 103.000 0.00 0.00
> ATOM 7 N NEU 7 23.000 33.000 103.000 0.00 0.00
> ATOM 8 C MP1 8 23.000 30.000 103.000 0.00 0.00
>
>
>
>
>
> --
> =====================================================
> Michael Brunsteiner, PhD
> Senior Researcher, Area II
> Research Center Pharmaceutical Engineering GmbH
> A-8010 Graz, Inffeldgasse 13
> phone: +43 316 873 30908
> mobile: +43 660 4887763
> fax: +43 316 873 109700
> e-mail: michael.brunsteiner at rcpe.at
> www.rcpe.at
> UID-Nr.: ATU64272307
> FN: 312899x, FB-Gericht: LG für ZRS Graz
>
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