Lei Zhou wrote:
Hi,
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?
You should never use epsilon_r other than 1, as your protein will
explode or implode.
You can use the vacuum force field, it makes sense in this case.
Thank you.
Lei Zhou
On 5/16/06, *Erik Lindahl* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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
<http://lorentz.immstr.pasteur.fr> .
Cheers,
Erik
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
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