[gmx-users] net charge correction

[Michael Brunsteiner]

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 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

?

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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