[gmx-users] Normal Mode Analysis

[Matthew Lardy]

Hi all,

Another quick question.  I have started performing normal mode analysis
(nma) of proteins from the PDB.  So they should already be in a minimum
energy configuration right?  If so how does one perform normal mode
analysis of a protein alone?  Assuming that I have already deleted
ligands, metal ions, and other proteins that might be in the pdb file.

What should the mdp file look like?  I have been using a mdp file that
looks like the following:

title                    = protein in water
cpp                      = /lib/cpp
include                  = -I../top
define                   = -DFLEX_SPC
integrator               = nm
emtol                    = 0.0001
emstep                   = 0.0001
nstcgsteep               = 10
nsteps                   = 10000
nstxout                  = 5
xtc_grps                 = Protein
energygrps               = Protein
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.4
vdwtype                  = Shift
coulombtype              = PME
rcoulomb                 = 1.4
rvdw                     = 1.4

For one, the nm run won't finish, not on my linux box at work.  :(  I dump
core about halfway through the run, a filesize limitation error of some
sort, so I figure I am making a major mistake before I start the run.
What is really interesting, is that I can complete the run on my Powermac
at home, but then I cannot diagonalize the matrix (that is a calloc error
there).  I know that I should have posted the output of these two dumps,
but I want to make sure that my general strategy is alright before I worry
any more about these other errors.

Thanks,
Matthew