[gmx-users] reference structure of g_rms
Hi Tsjerk, It's very helpful information. Thank you very much Sincerely yours, Hsin-Lin Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang : >> > Hi, >> > >> > I got confused about the choice of reference structure of g_rms. (g_rms >> > -s) >> > For example, >> > I run MD after PR. >> > That's means md.tpr was generated from pr.gro >> > I tried to use pr.gro and md.tpr to be the reference structure but get >> > different result. >> > I think these two should cause the same result. >> >> I think they should give the same result. If not, then the mostly likely >> explanation is that you've not used the files the way you think you have. >> You need to be able to issue >> >> grompp -f md -c pr -o md >> g_rms -s md.tpr -f whatever >> g_rms -s pr.gro -f whatever >> >> and get different results for there to be some kind of problem. In any >> case, you need to provide copies of your command lines and the different >> result in order for us to see whether you or GROMACS has done something >> wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do >> something else with our time :-) >> >> Mark > Hi, > > I checked the result again > The order of the different is less than 0.1 nm. > So that means this different is caused by precision? > > Sincerely yours, > Hsin-Lin > -- gmx-users mailing listgmx-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
Re: [gmx-users] reference structure of g_rms
Hi Hsin-Lin, If you use a .tpr file, you perform a mass-weighted fit and analysis. A .gro file has no masses and thus the fit and analysis are performed non-mass weighted, which will give differences, depending on the selection for the analysis. Hope it helps, Tsjerk 2011/8/17 Hsin-Lin Chiang : >> > Hi, >> > >> > I got confused about the choice of reference structure of g_rms. (g_rms >> > -s) >> > For example, >> > I run MD after PR. >> > That's means md.tpr was generated from pr.gro >> > I tried to use pr.gro and md.tpr to be the reference structure but get >> > different result. >> > I think these two should cause the same result. >> >> I think they should give the same result. If not, then the mostly likely >> explanation is that you've not used the files the way you think you have. >> You need to be able to issue >> >> grompp -f md -c pr -o md >> g_rms -s md.tpr -f whatever >> g_rms -s pr.gro -f whatever >> >> and get different results for there to be some kind of problem. In any >> case, you need to provide copies of your command lines and the different >> result in order for us to see whether you or GROMACS has done something >> wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do >> something else with our time :-) >> >> Mark > Hi, > > I checked the result again > The order of the different is less than 0.1 nm. > So that means this different is caused by precision? > > Sincerely yours, > Hsin-Lin > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing listgmx-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
[gmx-users] reference structure of g_rms
> > Hi, > > > > I got confused about the choice of reference structure of g_rms. (g_rms -s) > > For example, > > I run MD after PR. > > That's means md.tpr was generated from pr.gro > > I tried to use pr.gro and md.tpr to be the reference structure but get > > different result. > > I think these two should cause the same result. > > I think they should give the same result. If not, then the mostly likely > explanation is that you've not used the files the way you think you have. You > need to be able to issue > > grompp -f md -c pr -o md > g_rms -s md.tpr -f whatever > g_rms -s pr.gro -f whatever > > and get different results for there to be some kind of problem. In any case, > you need to provide copies of your command lines and the different result in > order for us to see whether you or GROMACS has done something > wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do > something else with our time :-) > > Mark Hi, I checked the result again The order of the different is less than 0.1 nm. So that means this different is caused by precision? Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-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
[gmx-users] reference structure of g_rms
> On 17/08/11, Hsin-Lin Chiang wrote: > > > Hi, > > > > I got confused about the choice of reference structure of g_rms. (g_rms -s) > > For example, > > I run MD after PR. > > That's means md.tpr was generated from pr.gro > > I tried to use pr.gro and md.tpr to be the reference structure but get > > different result. > > I think these two should cause the same result. > > I think they should give the same result. If not, then the mostly likely > explanation is that you've not used the files the way you think you have. You > need to be able to issue > > grompp -f md -c pr -o md > g_rms -s md.tpr -f whatever > g_rms -s pr.gro -f whatever > > and get different results for there to be some kind of problem. In any case, > you need to provide copies of your command lines and the different result in > order for us to see whether you or GROMACS has done something > wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do > something else with our time :-) > > Mark > Hi Mark, Thank you for your reply. I used, grompp -f md.mdp -c pr.gro -t pr.trr -o md.tpr mdrun -deffnm then, g_rms -f md.trr -s md.tpr -o rmsd1.xvg g_rms -f md.trr -s pr.gro -o rmsd2.xvg The output rmsd1.xvg and rmsd2.xvg are different in value. Hsin-Lin > > > > > > Could someone tell me what cause the different and which choice is > > better? > > > > And my version is gromacs v4.0.5 > > > > Sincerely yours, > > Hsin-Lin -- gmx-users mailing listgmx-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
Re: [gmx-users] reference structure of g_rms
On 17/08/11, Hsin-Lin Chiang wrote: > Hi, > > I got confused about the choice of reference structure of g_rms. (g_rms -s) > For example, > I run MD after PR. > That's means md.tpr was generated from pr.gro > I tried to use pr.gro and md.tpr to be the reference structure but get > different result. > I think these two should cause the same result. I think they should give the same result. If not, then the mostly likely explanation is that you've not used the files the way you think you have. You need to be able to issue grompp -f md -c pr -o md g_rms -s md.tpr -f whatever g_rms -s pr.gro -f whatever and get different results for there to be some kind of problem. In any case, you need to provide copies of your command lines and the different result in order for us to see whether you or GROMACS has done something wrong/unexpected/whatever. Otherwise it's hearsay and we'll shrug and do something else with our time :-) Mark > > > Could someone tell me what cause the different and which choice is better? > > And my version is gromacs v4.0.5 > > Sincerely yours, > Hsin-Lin > -- > gmx-users mailing listgmx-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 > > -- gmx-users mailing listgmx-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
[gmx-users] reference structure of g_rms
Hi, I got confused about the choice of reference structure of g_rms. (g_rms -s) For example, I run MD after PR. That's means md.tpr was generated from pr.gro I tried to use pr.gro and md.tpr to be the reference structure but get different result. I think these two should cause the same result. Could someone tell me what cause the different and which choice is better? And my version is gromacs v4.0.5 Sincerely yours, Hsin-Lin -- gmx-users mailing listgmx-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
