> On 17/08/11, Hsin-Lin Chiang <jian...@phys.sinica.edu.tw> 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
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