Hi Christian,
Perhaps, I made a mistake in describing my problem. I can not believe, that no
one ever tried this before.
I have a phosphate in water and want to calculate the hessian just for the
phosphate. How do I do that?
I have done something similar like what you want to do. I calculate the
hessian matrix of protein and some water surrounding (instead of all
waters). Then I diagonalize the sub-matrix which contains only the
coordinates of the protein. Here is the main part of my script:
---------------------------------------------------------------------
${dirr}/grompp_d -v -f ${dirh}/${nm}.mdp -c ${c}_yy.gro -o yy_${d}.tpr -p
${dirh}/${tops30}.top -np 1
mpirun -np 1 mdrun_d -s yy_${d}.tpr -mtx nm_w_${d}.mtx
mv nm_w_${d}.mtx nm_w_${d}.trj
trjconv_d -f nm_w_${d}.trj -s yy_${d}.tpr -o nm_nw_${d}.trj -fr
${dirh}/frame_36.ndx < ${dirh}/nm.p
mv nm_nw_${d}.trj nm_nw_${d}.mtx
g_nmeig_d -f nm_nw_${d}.mtx -s yy_${d}.tpr -o eigenval_${d}.xvg -v
x_${d}.trr
trjconv_d -f x_${d}.trr -s yy_${d}.tpr -o eigenvec_${d}.gro -b 1 <
${dirh}/nm.p
-------------------------------------------------------------------
You may also have a look at my paper:
JCP 119, 11350 (2003)
Hope it helps.
Phuong
Regards,
Christian
On Tuesday 19 June 2007 14:39, Christian Seifert wrote:
Hi.
I want to make a NMA just for one Group of molecules, because a QMMM-NMA
takes too long for the whole system. Of cause, the EM in the step before
has been done for the whole system. The manual does not tell how to do
this. Did someone tried this before?
Thanks
Christian.
--
B.Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: [EMAIL PROTECTED]
Web: http://www.bph.rub.de
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