Mark Abraham wrote:
pragya chohan wrote:
Dear Users
I am doing membrane simulation alternating nvt and npt during
production
run. After 1250 ps the water from upper leaflet goes towards the
lower
leaflet and a very thin layer of water remains in the upper
leaflet. Is
it a common occurance or am I doing some mistake?
Probably you are observing an artefact of periodic boundary
conditions -
see http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions for
advice here.
If you have set nstcomm=1, your bilayer should not experience a drift.
For some reason, however, the center of mass of the whole simulation
can slowly drift, even if explicit removal (nstcomm = 1) has been set.
This then looks as if just the bilayer would be drifting (or water
flowing
from one side of the bilayer to the other), although it actually is the
center of mass of the whole system.
A Bugzilla has been posted, please see
http://bugzilla.gromacs.org/show_bug.cgi?id=165
for further details.
Cheers,
Markus Miettinen
_______________________________________________
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
