[gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7)

[Mark Abraham]

Hi,

The default short-ranged scheme changed in 5.0, and it works differently. I
forget the details because both of these versions are long out of date.
What do you get with 2016?

Mark

On Thu, Jul 13, 2017 at 5:50 PM qiaobf <qiaobf at gmail.com> wrote:

> Dear All,
>
> I just got one problem with the energy printed by the g_energy. Could
> anyone help me with it? Thanks!
>
> In the test system, there is ONLY ONE trivalent metal (Me) and 2240
> modified TIP3P waters. After one MD step, I print the energies using
> g_energy. The results are:
>
> ** GROMACS 5.0.7 ************
>
> *Coul-SR:Me-Me              -521.008 *     -- 0          0  (kJ/mol)
> LJ-SR:Me-Me                       0                 -- 0          0
> (kJ/mol)
> Coul-SR:Me-SOL             -78.5025         --    30.1404 -60.2807
> (kJ/mol)
> LJ-SR:Me-SOL                195.268            --    104.218 -208.437
> (kJ/mol)
> Coul-SR:SOL-SOL             1958.38         --     452.82 -905.64  (kJ/mol)
> LJ-SR:SOL-SOL               91953.5           --    1966.23 -3932.45
> (kJ/mol)
>
> *********************************
>
> The weird thing is the Coul-SR: Me-Me is not zero, instead it is negative!
>
> Once I change the atomic charge of the trivalent metal from +3 to 0,
> this Coul-SR: Me-Me becomes zero.
>
> I also rerun the simulation using GROAMCS 4.5.5. The Coul-SR is zero
> (see below). But there exist some difference between the other energies
> between 5.0.7 and 4.5.5.
>
> ** GROMACS 4.5.5 ******************
>
> Coul-SR:Me-Me                     0            -- 0          0  (kJ/mol)
> LJ-SR:Me-Me                         0            -- 0          0  (kJ/mol)
> Coul-SR:Me-SOL             -57.4723      --          0          0 (kJ/mol)
> LJ-SR:Me-SOL                94.4865         --          0 0  (kJ/mol)
> Coul-SR:SOL-SOL             1771.36      --          0          0 (kJ/mol)
> LJ-SR:SOL-SOL               89843.4        --          0 0  (kJ/mol)
>
> **************************
>
>
> The topology and md.mdp files are listed below:
>
> ***** system.top *****************
>
> #include "charmm36-nov2016.ff/forcefield.itp"
>
> [ atomtypes ]
> ;type at.num  mass     charge ptype   sigma, nm  epsilon, kJ/mol
>   Me      1     1.000   0.0     A      3.385415e-01   2.092000e-01
>
> ;------------------------------ metal-----------------------
> [ moleculetype ]
> ; molname       nrexcl
>   Metal            1
>
> [ atoms ]
> ; id    at type       res.nr  residu.name     at.name  cg.nr  charge
> 1       Me            1       Me              Me       1       3.0
>
> #include "charmm36-nov2016.ff/tip3p.itp"
>
> [ system ]
> ; Name
> metal ion in water
>
> [ molecules ]
> ; Compound        #mols
>   Metal             1
>   SOL             2240
> *****************
>
> ****** md.mdp******
>
> ; Run control
> integrator               = md
> tinit                    = 0
> dt                       = 0.001
> nsteps                   = 1    ; 10ps
> nstcomm                  = 10
>
> ; Output control
> nstenergy                = 50
> energygrps               = ME SOL
>
>
> ; Neighborsearching and short-range nonbonded interactions
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.2
> ; Electrostatics
> coulombtype              = cutoff
> rcoulomb                 = 1.2
> ; van der Waals
> vdwtype                  = cutoff
> rvdw-switch              = 1.0
> rvdw                     = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr                  = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 1e-06
> epsilon_surface          = 0
>
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 298.15
>
> ; Pressure coupling is off for NVT
> Pcoupl                   = No
>
> ***************
>
>
>
> --
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