[gmx-users] Normal mode analysis

[Nguyen Hoang Phuong]

On Mon, 23 Jun 2003, Mark Fleharty wrote:

>
> Hello,
>
> Does anyone out there have any simple examples of normal mode analysis
> being performed with Gromacs?
>
> Thanks,
>
> Mark Fleharty

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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