[gmx-users] Hessian matrix conversion

[David van der Spoel]

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* <lindahl at sbc.su.se 
> <mailto: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
>     <http://lorentz.immstr.pasteur.fr> .
> 
>     Cheers,
> 
>     Erik
> 
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> 
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-- 
David.
________________________________________________________________________
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
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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