[gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 17 14:47:52 CET 2012

On 2012-03-17 14:44, qiancheng shen wrote:
> Hello Everyone,
> I‘m confused about Normal Mode Analysis of Gromacs. I have googled a lot
> but find little useful.
> I installed Gromacs 4.5.5 by CMake on Win7(Double Precision).
> Gromacs manual said "It is imperative that you use the |-t| option to
> |grompp <http://www.gromacs.org/Documentation/Gromacs_Utilities/grompp>|
> when you create the normal mode run input file
> <http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File>,
> so that you read full precision binary coordinates and not the
> three-decimal .gro
> <http://www.gromacs.org/Documentation/File_Formats/.gro_File> file." But
> I don't exactly what it means....
> Could anyone give me a step-by-step example?
> Thanks in advance.
> shen
grompp_d -f cg -o cg
mdrun_d -s cg -o conf.g96
grompp_d -f nm -c conf.g96 -o nm
mdrun_d -s nm

You can use the g96 coordinate format instead of using the trr file from 
the conjugate gradients energy minimization.
Set all cut-offs to zero (= infinite).

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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