[gmx-users] reference structure of g_rms

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Wed Aug 17 18:00:02 CEST 2011

> > 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 

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,
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