[gmx-users] Hessian matrix conversion

[Lei Zhou]

Hi,

Thank you for the answers. So I should use vacuum force field for the
all-atom NM analysis. But if I want to add a layer of explicit water
molecules as some papers did, which force field should I use?

Thanks you.

Lei Zhou



On 5/16/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> 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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