pragya chohan wrote:
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
Thanks I guess I was wrong. trjconv does write gro files.
In any case, working out
how to do the restart is
o put all
the water displaced back so that my initial rectangular structure is conserved.
> Date: Tue, 1 Jan 2008 14:41:09 +1100
> Subject: RE: [gmx-users] problem in bilayer simulation
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
>
>
>
>
> 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?
Depending on what you're doing, you may not need one. See
http://wiki.gromacs.org/inde
er 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
my next run?
> Date: Mon, 31 Dec 2007 08:17:15 +1100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] problem in bilayer simulation
>
> pragya chohan wrote:
> > Dear Users
> > I am doing membr
pragya chohan wrote:
can you please suggest what should i do? I have pbc = xyz in my md.mdp
I suggested that you read the link I provided. There's a strategy there
for managing what is probably only normal behavior that you are
perceiving as a problem.
People on mailing lists like this one
can you please suggest what should i do? I have pbc = xyz in my md.mdp> Date:
Mon, 31 Dec 2007 08:17:15 +1100> From: [EMAIL PROTECTED]> To:
gmx-users@gromacs.org> Subject: Re: [gmx-users] problem in bilayer simulation>
> pragya chohan wrote:> > Dear Users> >
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 mista
Does the water move through the bilayer, or is this a PBC thing? It sounds
like your bilayer is translating upwards?
- Original Message
From: pragya chohan <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Sunday, December 30, 2007 3:25:51 PM
Subject: [gmx-users] problem in bilayer s
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