[gmx-users] Fwd: Fwd: I have a symmetric simulation box

Christopher Neale chris.neale at mail.utoronto.ca
Fri Oct 19 02:12:20 CEST 2012

Try 100 ns of simulation. Also, note that g_density will not generally give you the correct result if you are using 
pressure coupling. This is because g_density builds the histogram up from z=0 to z=max and if you center 
your bilayer using pressure coupling then the center of the bilayer will not be at a constant z. To get this right
requires some additional trjconv preprocessing (see my earlier posts on this topic). Nevertheless, this is not
going to lead to massive asymmetry, so you are probably seeing something different.

As another note, you don't really seem to be doing a lot of work in composing your emails and checking
your system (e.g "more than bad" is not helpful for us at all). You'll get more out of this list if you put a little
bit more into checking your system and composing your emails to be as specific as possible.


Ali Alizadeh ali.alizadehmojarad at gmail.com 
Fri Oct 19 02:06:08 CEST 2012
Previous message: [gmx-users] A favor question: experience running Gromacs in the cloud
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---------- Forwarded message ----------
From: Ali Alizadeh <ali.alizadehmojarad at gmail.com>
Date: Fri, Oct 19, 2012 at 3:28 AM
Subject: Re: Fwd: I have a symmetric simulation box
To: Justin Lemkul <jalemkul at vt.edu>

Dear Justin

I ran my simulation for 8 nano second(1 ns to 8 ns) but my results was
more than bad,

my command for analysis of out put files:

g_density -f md.xtc -s md.tpr -dens number -o  dens2.xvg  -d z

xmgrace dens2.xvg


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