Hi Tsjerk
I think am lost now when you say 'filtered' which I don't know what it
means. Manual says:
-proj : calculate projections of a trajectory on eigenvectors
-extr : calculate the two extreme projections along a trajectory on the
average structure
Saying that analysis done on heavy atoms a
Hi Jio,
No, the 'extreme structures' are filtered along the eigenvector and are not
real structures. But you wanted the corresponding all-atom ones.
Cheers,
Tsjerk
On May 12, 2015 00:45, "gromacs query" wrote:
> Hi Tsjerk
>
> In -proj plot of v1 vs Time I used extreme values of V1 and saw stru
Hi Tsjerk
In -proj plot of v1 vs Time I used extreme values of V1 and saw structures
on those times. When I compare these structures to the structures obtained
from -extr the atomic positions (of 'same' extremes) are not 'exactly'
matching even after fitting. I tried with double precision as well.
Hi Jio,
You'll have to look at the projections (-proj), and see at which time these
have an extreme value.
Cheers,
Tsjerk
On Mon, May 11, 2015 at 11:00 PM, gromacs query
wrote:
> Hi Tsjerk
>
> Thanks for reply.
>
> >> So you can use the times
> I am unable to use it as explained below.
>
> I
Hi Tsjerk
Thanks for reply.
>> So you can use the times
I am unable to use it as explained below.
I get extremes output pdb like this:
g_covar -s avg.pdb -f all_frames.pdb
g_anaeig -s avg.pdb -extr two_extremes.pdb -first 1 -last 1 -nframes 2
Visually two structures in two_extremes.pdb looks
Hi Jio,
The scores for all-atom structures will be strongly correlated to those for
heavy-atom structures. So you can use the times for the heavy-atom extreme
projections to extract all-atom structures.
Cheers,
Tsjerk
On Mon, May 11, 2015 at 10:32 PM, gromacs query
wrote:
> Hi All
>
> I am do
Hi All
I am doing PCA and its working fine if I choose few atoms only (heavy) and
I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I
want to have extremes of all-atom structures, so I thought of doing PCA on
all-atoms but I end up with having Segmentation default error which
