[gmx-users] Hessian matrix conversion

Lei Zhou zhoumadison at gmail.com
Tue May 16 17:37:15 CEST 2006


Actually the major purpose was to extract the C-alpha components
from all-atom analysis, and then compare the result with other approaches,
like the PCA analysis or the GNM you mentioned. There was some discussion on
this before. I guess an easy way is still to use g_nmens to generate an
ensemble and run PCA on it?

I am still puzzled by an old question I have asked. For the all-atom NM
analysis, which force field is better, G43a1 or G43b1 (vacuum)? If I choose
the normal distribution (G43a1), maybe I should use an epsilon value of 2-4
with treatments of cut-off and rcoulomb=0?

Thank you.

Lei Zhou

On 5/16/06, Erik Lindahl <lindahl at sbc.su.se> wrote:
> Hi,
> On May 15, 2006, at 10:02 PM, Lei Zhou wrote:
> > Hi,
> >
> > I am trying to convert the binary Hessian matrix (nm.mtx) into a
> > readable ascii format. According to the recommendations on this
> > email list, I rename the nm.mtx to nm.trr and tried to use gmxdump.
> > However, there is an error message liketrn version:
> >
> > Program gmxdump, VERSION 3.3.1
> > Source code file: trnio.c, line: 69
> > Fatal error:
> > Float size 401. Maybe different CPU?
> >
> > I am using gromacs 3.3.1. Also I am wondering there is any new
> > update on the extration of C-alpha modes based on the all-atom
> > Hessian matrix? Thanks for the help.
> We had to discard the old Hessian format when introducing the sparse
> matrix representation to enable NMA for huge molecules. The easiest
> way to extract the data is probably to have a look in src/tools/
> gmx_nmeig.c.
> As for C-alpha modes, projections of orthogonal vectors onto a
> subspace won't be orthogonal in that subspace, so per definition they
> are not "normal" modes for C-alpha. If you really want Ca-only modes
> you are probably better of with an elastic network model online
> server, e.g. http://lorentz.immstr.pasteur.fr .
> Cheers,
> Erik
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