Dear All,
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's Website
and I am trying to convert the Atomistic structure to CG structure. For that
I am using atom2cg script provided by the martini folks but it doesn't
convert the Atomistic structure to CG structure. atom2cg script
sunny mishra wrote:
Dear All,
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's
Website and I am trying to convert the Atomistic structure to CG
structure. For that I am using atom2cg script provided by the martini
folks but it doesn't convert the Atomistic structure to CG
I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's
Website and I am trying to convert the Atomistic structure to CG
structure. For that I am using atom2cg script provided by the
martini folks but it doesn't convert the Atomistic structure to CG
structure. atom2cg script
Thanks for the reply. I have another quick question that If I have to do the
Position Restrained EM Simulation of CG DPPC lipid then is it done the same
way we do for atomistic structure of proteins like by defining the LIPPOSRES
in the lipid.mdp file or while using MARTINI forcefield is there any
No need of position restrained simulation with the CG lipids.
CG is very forgiving :))
For proteins it is more delicate.
On Dec 15, 2009, at 6:02 PM, sunny mishra wrote:
Thanks for the reply. I have another quick question that If I have
to do the Position Restrained EM Simulation of CG DPPC
Alright thanks. So should I do it for proteins?
On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole x.peri...@rug.nl wrote:
No need of position restrained simulation with the CG lipids.
CG is very forgiving :))
For proteins it is more delicate.
On Dec 15, 2009, at 6:02 PM, sunny mishra
Well if you put a protein CG into your DPPC bilayer you'll have to
be soft on the start. PR is one way to do it and you can do similar
to when doing on a atomistic simulation.
On Dec 15, 2009, at 6:13 PM, sunny mishra wrote:
Alright thanks. So should I do it for proteins?
On Tue, Dec 15,
ok. Thats the step where I am really confused that how to apply the PR on my
system file (system file is a combination of CG protein and CG lipid).
On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole x.peri...@rug.nl wrote:
Well if you put a protein CG into your DPPC bilayer you'll have to
be
For the steps to go through to have an embedded protein in
membrane bilayer Justin has made a nice tutorial ... look in
the mail list archive
On Dec 15, 2009, at 6:21 PM, sunny mishra wrote:
ok. Thats the step where I am really confused that how to apply the
PR on my system file (system file
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