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 <jiangsl at phys.sinica.edu.tw>: >> > 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 >
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