[gmx-users] NMA for a group

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Fri Jun 22 13:15:28 CEST 2007

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 

trjconv_d -f x_${d}.trr -s yy_${d}.tpr  -o eigenvec_${d}.gro -b 1  < 

You may also have a look at my paper:
JCP 119, 11350 (2003)

Hope it helps.


> 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: cseifert at bph.rub.de
> Web: http://www.bph.rub.de
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