Ah, OK. The commands I used were: g_msd -n POPC_index.ndx -lateral z -o POPC_150ns_CM_MSDlat.xvg -mol diffmol.xvg g_msd -n POPC_index.ndx -lateral z -o POPC_150ns_MW_MSDlat.xvg
> > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111208/0d0d66d6/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 09 Dec 2011 12:36:49 +1100 > From: Mark Abraham <mark.abra...@anu.edu.au> > Subject: Re: [gmx-users] Re:Re:Re: MSD normalization > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4ee16631.2030...@anu.edu.au> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 9/12/2011 5:37 AM, Sławomir Stachura wrote: >> 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. > > OK, but we need to see your terminal command lines in order to eliminate > your use of the tool as a source of the problem. They should be at the > top of the .xvg file, if nowhere else. > > Mark > >> >> 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
