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<font size="2">Hi Tsjerk,
<br />
<br />It's very helpful information.
<br />Thank you very much
<br />
<br />Sincerely yours,
<br />Hsin-Lin
<br />
<pre>Hi
Hsin-Lin,
If you use a .tpr file, you perform a mass-weighted fit and
analysis.
A .gro file has no masses and thus the fit and analysis are
performed
non-mass weighted, which will give differences, depending on
the
selection for the
analysis.
Hope it
helps,
Tsjerk
2011/8/17 Hsin-Lin Chiang <<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">jiangsl at
phys.sinica.edu.tw</a>>:
>><i> >
Hi,
</i>>><i>
>
</i>>><i> > I got confused about the choice of reference structure of
g_rms.
(g_rms
</i>>><i> >
-s)
</i>>><i> > For
example,
</i>>><i> > I run MD after
PR.
</i>>><i> > That's means md.tpr was generated from
pr.gro
</i>>><i> > I tried to use pr.gro and md.tpr to be the reference
structure but
get
</i>>><i> > different
result.
</i>>><i> > I think these two should cause the same
result.
</i>>><i>
</i>>><i> I think they should give the same result. If not, then the
mostly
likely
</i>>><i> explanation is that you've not used the files the way you think
you
have.
</i>>><i> You need to be able to
issue
</i>>><i>
</i>>><i> grompp -f md -c pr -o
md
</i>>><i> g_rms -s md.tpr -f
whatever
</i>>><i> g_rms -s pr.gro -f
whatever
</i>>><i>
</i>>><i> and get different results for there to be some kind of problem.
In
any
</i>>><i> case, you need to provide copies of your command lines and the
different
</i>>><i> result in order for us to see whether you or GROMACS has done
something
</i>>><i> wrong/unexpected/whatever. Otherwise it's hearsay and we'll
shrug and
do
</i>>><i> something else with our time
:-)
</i>>><i>
</i>>><i>
Mark
</i>><i>
Hi,
</i>><i>
</i>><i> I checked the result
again
</i>><i> The order of the different is less than 0.1
nm.
</i>><i> So that means this different is caused by
precision?
</i>><i>
</i>><i> Sincerely
yours,
</i>><i>
Hsin-Lin
</i>>
</pre>
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