Mark,
By 'coverage' I mean the 1 value in the dot product of the comparing
eigenvectors sets (between 1 and 1, 2 and 2 and so on eigenvectors) (
that indicate that both eigenvector set are identical as I suppose).
In that case I had 2 identical pdp ensembles from which in 1 case I
obtained normal
On Fri, Jan 25, 2013 at 6:40 AM, James Starlight wrote:
> Mark,
>
> as I told previously to Justin ( lets to consider the problems with
> g_anaeig only in that topic to avoid producing doubles ) the problem
> is not in the average structure (it looks fine)
You might have noticed I made no mentio
Mark,
as I told previously to Justin ( lets to consider the problems with
g_anaeig only in that topic to avoid producing doubles ) the problem
is not in the average structure (it looks fine) but in the
filter.xtc trajectory produced by g_anaeig. When I load that xtc to
any structure in vmd I obtai
On Tue, Jan 22, 2013 at 8:22 PM, James Starlight wrote:
> Dear Gromacs users!
>
>
> There is some bug with g_anaeig the souce of which I could not fully
> understand.
Good Advice: until you can almost write a code patch to fix it, be very
hesitant in suggesting any software has a bug. The best
Dear Gromacs users!
There is some bug with g_anaeig the souce of which I could not fully
understand. I have problems when I perform PCA of X-ray data set.
Below you can my workflow.
g_covar -f b2ar_xray_coors.pdb -s ref.pdb -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last
Ok, I've found the problem. It was my stupid mistake -
I forget that the filtered trajectory contains only CA
:) Thank you for help!
--- David van der Spoel <[EMAIL PROTECTED]> wrote:
> Semen Esilevsky wrote:
> >>You have to use also a reference file with the
> same
> >>amount of atoms in it,
>
Semen Esilevsky wrote:
You have to use also a reference file with the same
amount of atoms in it,
like your new trajectory.
Use something like trjconv or as the error msg say
tpbconv to write out a
gro/pdb file only with CA atoms.
No, this is not an issue here. I've made the same but
witho
> You have to use also a reference file with the same
> amount of atoms in it,
> like your new trajectory.
>
> Use something like trjconv or as the error msg say
> tpbconv to write out a
> gro/pdb file only with CA atoms.
No, this is not an issue here. I've made the same but
without -ref option
hi,
On Tuesday 18 July 2006 12:12, Semen Esilevsky wrote:
> Dear gmx users,
> I've found a strange problem in g_anaeig.
> I'm trying to project the trajectory into few first
> eigenvectors. For this I first do:
>
> g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit
> -ref -pbc -tu ns
>
> Chosing C
Dear gmx users,
I've found a strange problem in g_anaeig.
I'm trying to project the trajectory into few first
eigenvectors. For this I first do:
g_covar -f md_all.xtc -s md0.tpr -n index.ndx -fit
-ref -pbc -tu ns
Chosing CA group for matrix construction.
Then I pick the resulting file eigenvec.t
10 matches
Mail list logo
