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 <[EMAIL PROTECTED]> 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* <[EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>> 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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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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