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

[David van der Spoel]

On 2012-03-17 15:34, qiancheng shen wrote:
> Dear David:
> Thank you very much!! I'm really new to Gromacs.
> I think I should use the *.trr file(from mdrun_d, energy minimization)
> as an input file for generating *.tpr for Normal Mode Analysis.

Please read my previous email.

> But what the *.mdp file looks like while using "grompp_d -f nm -c
> conf.g96 -o nm" to make such *.tpr file?
>
integrator = nm

> I appreciate your help.
>
> Shen
>
> 在 2012年3月17日 下午9:47，David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>写道：
>
>     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
>         <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
>         <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
>         <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
>     g_nmeig_d
>
>     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 <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
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-- 
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