Hi Bob,
This would give an intolerable decrease in performance, because of the
neighbour searching thing.
I had a routine which might be of help, but unfortunately somewhere in
the process of "improvement" I broke it and didn't return to it again.
Maybe I can have a look at it some moment these days (but don't expect
it to be a panacee).
Best,
Tsjerk
On 3/15/07, Robert Johnson <[EMAIL PROTECTED]> wrote:
Hello everyone,
As I was discussing in a previous thread, I'm having problems
visualizing/analyzing an REMD trajectory of ssDNA. As I understand,
most tools for unwrapping PBC (i.e. removing the jumps from one side
of the box to the other) do so by detecting large displacements
between successive frames. These large displacements are then
considered jumps which are corrected for accordingly.
These tools do not work for REMD because this type of trajectory is
riddled with large displacements - both from atoms jumping across the
box but also due to the swaps between adjacent replica. Using these
tools on REMD trajectories leads to detection of erroneous jumps.
The easiest thing to do (in principle anyway) would be to modify
Gromacs so that it would write coordinates outside the primary
periodic box (i.e. not apply periodic wrapping to the coordinates).
Has anyone done this? If not, can anyone give me some pointers on
where to start?
Thanks,
Bob Johnson
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
