[gmx-users] Hessian matrix conversion
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 16 20:07:22 CEST 2006
Lei Zhou wrote:
> 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?
>
Depends on how much water :)
Maybe read those papers a bit more carefully, but in that case full
charges would be OK too I'd say.
> Thanks you.
>
> Lei Zhou
>
>
>
> On 5/16/06, *David van der Spoel* <spoel at xray.bmc.uu.se
> <mailto: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>
> > <mailto: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
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > <mailto: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> > <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> >
> ------------------------------------------------------------------------
>
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> 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
> <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> <mailto:spoel at gromacs.org> http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> <http://www.gromacs.org/mailman/listinfo/gmx-users>
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list