[gmx-users] reference structure of g_rms

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Wed Aug 17 17:49:02 CEST 2011

> On 17/08/11, Hsin-Lin Chiang <jiangsl at 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&#160;&#160;&#160;&#160;&#160; 
mdrun -deffnm

g_rms -f md.trr -s md.tpr -o rmsd1.xvg
g_rms -f md.trr -s pr.gro&#160; -o rmsd2.xvg

The output rmsd1.xvg and rmsd2.xvg are different in value.

> > 
> > 
> > Could someone tell me &#160;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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