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

[qiancheng shen]

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

       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>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    http://folding.bmc.uu.se
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