[gmx-users] problem in bilayer simulation

[Alan Dodd]

I'm going to assume you've read http://wiki.gromacs.org/index.php/Doing_Restarts.
I suggest you also look more closely at the manual page for trjconv.

----- Original Message ----
From: pragya chohan <pragyachohan at hotmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, December 31, 2007 1:56:41 PM
Subject: RE: [gmx-users] problem in bilayer simulation



I think you misunderstood my reply. 
I understood that it is a periodic boundry condition problem and used trjconv. But it writes a trajectory file. How do I make a gro file to input it into next run? I cant even use tpbconv command because trjconv writes a xtc file and I need a trr file for my next run?

----------------------------------------
> Date: Mon, 31 Dec 2007 08:17:15 +1100
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem in bilayer simulation
> 
> 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.
> 
> Mark
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