[gmx-users] ffgmx:diffusion of oxygen

[Mark Abraham]

Sunil Thapa wrote:
> Respectable Justin/David/Mark
> I used ffgmx force field thinking it as suitable for bonds in the oxygen 
> molecule. And yes it gives diffusion coefficient of SPC water to be 3.5 
> which matches with that given in the gromacs manual. After equilibrating 
> my system of 1 oxygen and 255 water molecules in NPT ensemble at 1 bar 
> and 298 K i subjected it to the NVT ensemble for about 50 ns. The msd is 
> not a straight line. It increases linearly for first 20 ns and after 
> some ns it decreases linearly giving negative diffusion coefficient. 
> Could you help me out with it? The model contains L-J interaction 
> between oxygen and water molecule. The mdp file used for production run 
> is as follows:
> ;RUN CONTROL parameters.
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 50000000 ; total 1 ns.
> nstcomm = 1
> ;LANGEVIN DYNAMICS parameters have not been specified as the integrator is
> ;md
> ;OUPUT CONTROL parameters.
> nstxout = 250
> nstvout = 1000
> nstfout = 0
> nstlog = 100
> nstenergy = 100
> energygrps = OMOL SOL
> ;NEIGHBOUR SEARCHING parameters.
> nstlist = 10
> ns_type = grid
> rlist = 0.9 ;initially 1 I modified to 0.9
> ;ELECTROSTATIC and VdW parameters.
> rcoulomb = 0.9
> rvdw = 0.9
> epsilon-r = 1
> ;BERENDSEN TEMPERATURE COUPLING is on in two groups
> Tcoupl = berendsen
> tc-grps = OMOL SOL

http://wiki.gromacs.org/index.php/Thermostats

> tau_t = 0.001 0.01
> ref_t = 298 298
> ;PRESSURE COUPLING is on
> Pcoupl = no;berendsen; berendsen exponential relaxation coupling
> tau_p = 0.1;modified from 0.5
> compressibility = 4.6e-5
> ref_p = 1.0
> ;SIMULATED ANNEALING parameters are not specified.
> ;GENERATE VELOCITIES is on at 298 K.
> gen_vel = no; ; generate initially
> gen_temp = 298
> gen_seed = 173529 ;give different values for different trials.
> ;BONDS parameters
> constraints = all-bonds
> constraint-algorithm = shake
> unconstrained-start = yes
>  
> and the msd curve is attached in the next mail due to insufficient space
> Your help is necessary for me.
> Sunil Kumar Thapa
> Tribhuvan University, Nepal
>  
>  
> 
> 
> 
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