[gmx-users] gromacs electrostatic energy

[David van der Spoel]

On 31/07/16 05:23, 王珍 wrote:
> Hi all, I use two methods to calculate the electrostatic energy of two atoms of RNA.

what do you mean "two atoms of RNA"?
And what is the physical meaning of "electrostatic energy"?

> Firstly, when I use the g_enengy to calculate the electrostatic energy in gromacs.
g_energy does not compute any energies. It just reports what is in the 
.edr file coming from your simulation.


> Secondly, I just use the formula of electrostatic energy (E=f*q(i)*q(j)/r),
> The results of two methods make a great difference. For gromacs, the algorithm of electrostatic energy is not the (E=f*q(i)*q(j)/r) ?
>
> Thank you very much.
>
> The following is the file of mdp.
> title               =  1ZIH
> cpp                 =  /lib/cpp
>
> ;run parameters
> integrator          =  md
> dt                  =  0.002                    ; ps
> nsteps              =  2                ; total 1ns
> nstcomm             =  100
> define              = -DPOSRES
>
> ;output control
> nstxout             =  1000                     ; collect data every 2 ps
> nstxtcout           =  1000
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  1000
> nstcalcenergy       =  1                     ;frequency fo calculating the energy
> nstenergy           =  1000                    ;frequency to write energies to energy file
>
> ;Bond parameter
> continuation           = yes                     ;restarting after NPT
> constraint-algorithm   = lincs
> constraints            = all-bonds               ;none
> lincs_iter             = 1
> lincs_order            = 4
>
> ;Neighborsearching
> ns_type             =  grid
> nstlist             =  10
> rlist               =  1.0
> rcoulomb            =  1.0
> vdwtype             =  cut-off
> rvdw                =  1.0
>
> ;Electrostatics
> coulombtype         =  PME
> pme_order      =  4
> fourierspacing      =  0.12
>
> ;Temperature coupling is on
> Tcoupl              = V-rescale                     ;berendsen
> tc-grps             = system
> Tau_t               = 0.1
> ref_t               = 300
>
> ; Berendsen Pressure coupling is on
> Pcoupl              = Parrinello-Rahman
> Pcoupltype          = isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-05
> ref_p               =  1.0
>
> ;Periodic boundary conditions
> pbc                 = xyz
>
> ;Dispersion correction
> DispCorr            = EnerPres
> refcoord_scaling    = all
> ; Generate velocites
> gen_vel             =  no
>
> energygrps = a115 a17
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se