Hi! Thanks Mark for reply. When I calculated fractional diffusion constant from mass weighted MSD of long simulation I get sth about 0.05. But when I do the same for centre of mass, considering that MSD is expressed in nm^2, the result is 1.35. When I look into xvg file MSD of centre of mass is 10-20 times than for mass-weighted (which is substantially wrong). So assuming that, by any chance, centre of mass MSD is in A^2, calculated fractional diffusion constant is of 0.02 magnitude, which is theoretically more understandable. What I can show you is a sample of two MSDs:
- Mass weighted: 0 0 15 0.0150352 30 0.0198877 45 0.0235849 60 0.0267214 75 0.0294651 90 0.0319853 105 0.0342538 120 0.0364239 135 0.0384275 150 0.0403661 165 0.0421938 180 0.0439495 195 0.0456557 210 0.0472885 225 0.0488768 240 0.0503814 255 0.051868 270 0.0533207 285 0.0547436 300 0.0561625 -And centre of mass: 0 0 15 0.916885 30 1.05944 45 1.16649 60 1.25004 75 1.31444 90 1.37307 105 1.43301 120 1.47879 135 1.52776 150 1.57137 165 1.6211 180 1.64439 195 1.68883 210 1.71222 225 1.75035 240 1.77255 255 1.8117 270 1.83702 285 1.87376 300 1.8958 But still there is more thing - do you how the MSD is normalized? Because I have compared mass weighted MSD calculated using Gromacs tool and nMoldyn and I get the same difference for all my cases (simulations of 2ns, 15ns and 150ns)- in the latter diffusion constant is twice the value of the one obtained in Gromacs. So I expect the difference in normalization. Cheers, Slawomir > > On 6/12/2011 3:58 AM, S“awomir Stachura wrote: >> Hi, >> >> There is something interesting concerning these MSD calculations. If I treat >> Centre of Mass MSD if it'd be expressed not in nm^2/ps , but >> Angstroms^2/ps, I get ideally the same results as for mass-weighted ones. >> And it's true for all my three cases, in which I performed simulation of >> different times. Is that possible there is some bug in MSD? Because as for >> me it looks so.... > > I would be amazed if GROMACS did this. Can you copy and paste from your > terminal to show this? > > Mark > >> Hope to have someone join the discussion, >> Slawomir >> >> >> >> >> >> Wiadomo¶æ napisana przez S“awomir Stachura w dniu 2011-12-04, o godz. 22:38: >> >>> Hi, >>> >>> I was just wondering how MSDs in Gromacs are normalized. I am calculatiing >>> MSDs for my lipid system of different timesteps of simulation and I get >>> much higher results for centre of mass calculations in comparison to >>> mass-weighted one. And I thought about normalization issue, but I couldn't >>> find any informations concerning that topic in manual. >>> I'd be grateful if someone could explain how mean square displacement is >>> normalized. >>> >>> Cheers, >>> Slawomir > -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists