[gmx-users] non-zero Coul-SR interaction between metal ion in the system with only one metal (GMX 5.0.7)
Mark Abraham
mark.j.abraham at gmail.com
Thu Jul 13 20:01:13 CEST 2017
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forget the details because both of these versions are long out of date.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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