> > 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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