Dear all,
by doing MD simulations of a protein complex embedded in 2 membranes
(inner and outer membrane of bacteria, POPE), we observe a bilayer
splitting in one of the membranes. This has the effect that the bilayer
forms "bubbles" with vacuum inside.
It might have something to do with the PME
Forwarded Message
From: Thomas Schmidt
Reply-To: schm...@bit.uni-bonn.de
To: mishra.su...@gmail.com
Subject: Re: Inflategro for Coarse Grained
Date: Thu, 29 Oct 2009 13:45:02 +0100
Dear Sunny,
Justin's right.
The definition of the lipid-representative atom (P) is do
pping. For other molecules you have to do it
> your self by hand, following examples given in the workshop
> would be the best ...
>
> On Oct 26, 2009, at 2:13 PM, Thomas Schmidt wrote:
>
> > Dear all,
> >
> > how can I create the mapping section for "g_fg2cg&quo
Dear all,
how can I create the mapping section for "g_fg2cg" in the atomistic
*.itp file? The handout from the Coarse Graining Workshop 2009 says that
pdb2gmx has this ability but I can't find it:
http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/CGWS_Tutorial.pdf/download.
By
n purpose, if needed.
>
> Cheers,
> Nicolas
>
>
> Thomas Schmidt a écrit :
> > Dear Omer,
> >
> > many thanks for your answer, but your solution doesn't work for me.
> > We have Protein-Lipid models in the CG scale.
> > Only if I replace all ato
ovitch wrote:
> What I do is visualize as trace. Than all the coarse-grained sphere
> are connected. Hope it helps. Omer.
>
> Koby Levy research group,
> Weizmann Institute of Science.
> FAX: 972-77-444-7905
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>
>
>
Dear all,
is there any possibility to give the bond information out of GROMACS
files to VMD? Especially for coarse-grained models (using the MARTINI
FF) this would be a nice feature for visualization.
But in that case the distance analysis doesn't work, because we will
always have too high distan
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