[gmx-users] SR-coulomb energy

[SANTU BISWAS]

Dear users,

                I have performed an simulation of polypeptide(5-residues of
alanine) in vacuum using gmx_4.5.5 (Double Precision). For this, I am using
all cutoff=0 with no pbc. The input mdp file for the simulation is given
below

title                    = peptide in vaccum
cpp                      = /lib/cpp
define                   = -DFLEXIBLE
; RUN CONTROL
integrator               = md
comm_mode          = ANGULAR
nsteps                   = 1000000
dt                          = 0.0005
; NEIGHBOR SEARCHING
nstlist                  = 0
ns_type               = simple
pbc                     = no
rlist                     = 0
; OUTPUT CONTROL
nstxout                  = 1000
nstvout                  = 1000
nstxtcout                = 0
nstlog                   = 1000
constraints              = none
nstenergy                = 1000
; OPTION FOR ELECTROSTATIC AND VDW
rcoulomb                 = 0
; Method for doing Van der Waals
rvdw                     = 0
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl                   = V-rescale
tc_grps                  = Protein
tau_t                    = 0.1
ref_t                    = 300



The output (.log) file is

    Step           Time         Lambda
              0        0.00000        0.00000

Group rest with mass  4.28491e+02, Ekrot  6.48028e+00 Det(I) =  4.27209e+03
  COM:      1.82773       1.85017       1.82461
  P:        0.00000      -0.00000       0.00000
  V:        0.00000      -0.00000       0.00000
  J:       -0.82095     -13.54870     -19.02024
  w:        0.02012      -0.41432      -0.38715
Inertia tensor (3x3):
   Inertia tensor[    0]={ 1.34454e+01, -6.11374e+00,  2.21534e+00}
   Inertia tensor[    1]={-6.11374e+00,  2.88115e+01, -6.31417e+00}
   Inertia tensor[    2]={ 2.21534e+00, -6.31417e+00,  1.36527e+01}
   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    4.93368e+00    1.49038e+01    1.00713e+00    3.83183e+01    7.57789e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)      Potential    Kinetic En.
    7.82758e+02   -6.47030e+01   -1.48187e+03   -6.28870e+02    2.30892e+02
   Total Energy  Conserved En.    Temperature Pressure (bar)
   -3.97978e+02   -3.97978e+02    3.08553e+02    0.00000e+00
gen_vel                  = yes
gen_temp                 = 300

Now the problem is with Coulomb (SR) value.To check this value, I have
calculated coulomb interactions beyond 1-4 interaction by the following
equation

energ=(f*q1*q2)/r ; where f=138.935485

but the value which I obtain for step 0 is -170.10733 and this not the same
as the log file. I do not know how Gromacs calculate coulomb (SR) value.
Please suggest if I am missing something.

Thanks
Santu