xRe: [gmx-users] Normal mode analysis

[Mark Fleharty]

Thanks Nguyen for the normal mode example.  I tried to get this to work,
but was unable.  I created a .tar file and attatched it.  When I run
grompp, it complains that I do not have a .top file.

Thanks,

Mark Fleharty

On Tue, 24 Jun 2003, Nguyen Hoang Phuong wrote:

> Hi,
>
> here are the simple commands used for NMA performed with Gromacs:
>
> grompp_d -v -f nm.mdp -c xxx.gro -o xxx.tpr -p xxx.top
>
> mdrun_d -s xxx.tpr -mtx nm.mtx
>
> g_nmeig_d -f nm.mtx -s xxx.tpr -o eigenvalue.xvg -v eigenvector.trr
>
> trjconv_d -f eigenvector.trr -s xxx.tpr  -o eigenvector.gro
>
> At the end you will get the eigenvalues (related to normal mode
> frequencies) stored in the file eigenvalue.xvg (in readable format)
> and the eigenvectors in eigenvector.trr. If you want to read this
> file, you have to convert it to readable format, using the last command.
>
> Here is the nm.mdp file:
>
> title                    = xxxx
> cpp                      = /lib/cpp
> include                  = -I../top
> define                   =
> integrator               = nm
> emtol                    = 0.000001
> emstep                   = 0.000001
> nstcgsteep               = 1000
> nsteps                   = 500000
> nstxout                  = 50
> xtc_grps                 = Protein
> energygrps               = Protein
> nstlist                  = 10
> ns_type                  = grid
> rlist                    = 1.
> vdwtype                  = Shift
> coulombtype              = cut-off
> rcoulomb                 = 0.
> rvdw                     = 0.
> pbc                      = no
>
> Here is xxx.gro file:
>
> Protein in water
>   22
>     1ALA      N    1   1.004   1.392   0.821
>     1ALA     H1    2   1.025   1.300   0.785
>     1ALA     H2    3   0.922   1.427   0.774
>     1ALA     H3    4   1.081   1.454   0.799
>     1ALA     CA    5   0.981   1.389   0.967
>     1ALA     CB    6   0.884   1.276   1.000
>     1ALA      C    7   1.114   1.369   1.042
>     1ALA      O    8   1.209   1.317   0.985
>     2ALA      N    9   1.120   1.415   1.167
>     2ALA      H   10   1.040   1.454   1.216
>     2ALA     CA   11   1.245   1.414   1.246
>     2ALA     CB   12   1.282   1.558   1.284
>     2ALA      C   13   1.247   1.327   1.373
>     2ALA      O   14   1.147   1.309   1.442
>     3ALA      N   15   1.359   1.255   1.385
>     3ALA      H   16   1.398   1.214   1.302
>     3ALA     CA   17   1.404   1.194   1.513
>     3ALA     CB   18   1.423   1.043   1.493
>     3ALA      C   19   1.533   1.255   1.571
>     3ALA     OT   20   1.546   1.271   1.692
>     3ALA      O   21   1.635   1.294   1.489
>     3ALA     HO   22   1.701   1.342   1.552
>    4.85000   4.85000   4.85000
>
>
> Hope this help.
>
> Phuong
>
> >
> >
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