Thanks for the insights, Tsjerk. I figured it was something to do with the new
algorithm; just wanted to confirm that this was the expected behavior.
Indeed, trjconv is one's friend in such a case :)
-Justin
Tsjerk Wassenaar wrote:
Hi Justin,
It's indeed the case that mdrun now writes broken molecules. Has to do
with the domain decomposition and processors only keeping track of
'their' atoms. Too bad, but you'll just have to keep a .tpr around to
make molecules whole again afterwards. Using trjconv -nojump with a
suitable reference (not necessarily a .tpr) would also do it (and
simultaneously remove the jumps...).
Cheers,
Tsjerk
On Sun, Oct 5, 2008 at 4:32 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
Hi,
I've been running some simulations with Gromacs 4.0 RC2, and I've noticed
something strange. In the output .gro file at the end of a run, the
molecules in my system (a membrane protein) are broken, crossing periodic
boundaries. This affects the lipids at the periphery of the box, in my case.
Has there been some change since the previous version that mdrun is now
writing broken molecules to fit everything within the unit cell? Or is this
behavior unintentional?
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
