[gmx-users] Re: problem in bilayer simulation

[Markus Miettinen]

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