Could it be that you have not removed the jumps due to the periodic boudary conditions before using g_msd?
Try trjconv -pbc nojump Jochen 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 > 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 > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
