[gmx-users] ffgmx:diffusion of oxygen
David van der Spoel
spoel at xray.bmc.uu.se
Mon Apr 27 14:31:49 CEST 2009
Jochen Hub wrote:
> Could it be that you have not removed the jumps due to the periodic
> boudary conditions before using g_msd?
> trjconv -pbc nojump
> 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:
This is probably due to poor statistics. g_mds corrects for PBC.
Simulate a few 100 ns, then you know more.
>> ;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
>> ;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
>> 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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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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