[gmx-users] !Help!: Normal Mode Analysis

[Yu Ogawa]

Hi,
I am not an expert, but I think there is no such tricky parameter for
normal mode calculation though I don't know what your situation is..
You can find some tips at the below link..
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis

If you set parameters extremely wrong the grompp program gives some notes
and warnings that would help you a lot. An important thing is that you have
to perform all the calculations with double precision.

Yu




2014-07-29 15:37 GMT+02:00 xy21hb <xy21hb at 163.com>:

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> Dear all,
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> I wonder if there is anywhere I can know the details of mdp files used for
> normal mode analysis.
> I understand from the maunal that it needs steepest descent, conjugate
> gradient, l-bfgs, nm in "md" options consecutively,
> but I am not sure about other parameters set in these different stages.
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> Many thanks,
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> OAY
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