Hi, you already have your solution at hand.
On 10.02.2010, at 10:05, Amit Choubey wrote: > Hi Everyone, > > I have been trying to calculate diffusion coefficient for water. I am trying > to reproduce the numbers published in journal papers. > I am using SPCE water model. I use the g_msd analysis tool. > > g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8 > > I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I > equilibriate the system for a ns and then run for additional 10 ps for > analysis. Here are some of the numbers that i get > > a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/- 0.2992) > 1e-5 cm^2/s > b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/- > 0.1076) 1e-5 cm^2/s > c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P > coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s . > > c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s but > its not quite right. > You obtain a quite good estimation of the diffusion coefficient when not applying the Berendsen coupling scheme. The reason for this is that Berendsen coupling does not allow to generate a correct thermodynamic ensemble. Applying v-rescale or Nose-Hoover in combination with Parrinello-Rahman should yield more accurate results, because the take the way of sampling the phase space in an appropriate manner into account. Cheers, Flo > Could someone explain to me why the values obtained in above 3 cases are > widely different and may be give some tips about the right procedure to > calculate diffusion (method and invoking the g_msd tool)? > > Thank you > Amit > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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