<HTML>
<HEAD>
<META content="text/html; charset=big5" http-equiv=Content-Type>
<META content="OPENWEBMAIL" name=GENERATOR>
</HEAD>
<BODY bgColor=#ffffff>
<font size="2"><b></b>>
On 17/08/11, Hsin-Lin Chiang <jiangsl@phys.sinica.edu.tw> wrote:
<br />>
<br />>
> Hi,
<br />>
>
<br />>
> I got confused about the choice of reference structure of g_rms. (g_rms -s)
<br />>
> For example,
<br />>
> I run MD after PR.
<br />>
> That's means md.tpr was generated from pr.gro
<br />>
> I tried to use pr.gro and md.tpr to be the reference structure but get
different result.
<br />>
> I think these two should cause the same result.
<br />>
<br />>
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
<br />>
<br />>
grompp -f md -c pr -o md
<br />>
g_rms -s md.tpr -f whatever
<br />>
g_rms -s pr.gro -f whatever
<br />>
<br />>
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 :-)
<br />>
<br />>
Mark
<br />>
<br />Hi Mark,
<br />
<br />Thank you for your reply.
<br />I used,
<br />grompp -f md.mdp -c pr.gro -t pr.trr -o md.tpr     
<br />mdrun -deffnm
<br />
<br />then,
<br />g_rms -f md.trr -s md.tpr -o rmsd1.xvg
<br />g_rms -f md.trr -s pr.gro  -o rmsd2.xvg
<br />
<br />The output rmsd1.xvg and rmsd2.xvg are different in value.
<br />
<br />Hsin-Lin
<br />>
>
<br />>
>
<br />>
> Could someone tell me  what cause the different and which choice is
better?
<br />>
>
<br />>
> And my version is gromacs v4.0.5
<br />>
>
<br />>
> Sincerely yours,
<br />>
> Hsin-Lin
<br />
<br />
</font>
</BODY>
</HTML>