From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of anu chandra
[anu80...@gmail.com]
Sent: 22 June 2015 11:10
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] membrane model
Thanks to all for the useful replies. BTW, which force field will be good
option for simulating united-atom (acyl chain) POPC membranes?
Many thanks
Anu
On Fri, Jun 19, 2015 at 5:15 PM, Thomas Piggot wrote:
> Good to see the membrane structures have been changed/fixed. I think it
> was December
for lipids and surfactants. J. Phys. Chem. B
2014, 118, 547–56.
Best
--
Message: 4
Date: Fri, 19 Jun 2015 15:52:14 +0100
From: anu chandra
To: Discussion list for GROMACS users
Subject: [gmx-users] membrane model
Message
Good to see the membrane structures have been changed/fixed. I think it
was December 2010 when I last downloaded the POPC one!
I did port over the lipid parameters for C27-UA a good while ago but
haven't got around to the C36-UA parameters yet.
On 19/06/15 16:55, Justin Lemkul wrote:
On 6/
On 6/19/15 11:38 AM, Thomas Piggot wrote:
Well, the CHARMM ff is not entirely all-atom:
http://pubs.acs.org/doi/abs/10.1021/jp410344g
True, people have developed UA force fields from CHARMM's all-atom models. My
comment was largely motivated by the fact that the official CHARMM36 port for
Well, the CHARMM ff is not entirely all-atom:
http://pubs.acs.org/doi/abs/10.1021/jp410344g
As for downloading the structure, I would be slightly careful with the
link that Justin provided for POPC as (well, based upon the last time I
used it anyway) there were a different number of lipids in
Dear Justin,
Thanks for the inputs. May I know which force field can be a good option
for united atom (acyl chain) POPC?. A recent article (
http://pubs.acs.org/doi/abs/10.1021/jp401403b) says CHARMM27 united atom
model is adopted for POPC. Unfortunately the web-link you mentioned here
have only t
On 6/19/15 10:52 AM, anu chandra wrote:
Dear Gromacs users,
I am planing to do a protein simulation in acyl chain united-atom POPC
membrane model. It will of great help if few of my queries regarding
setting up the system get answered.
1. Which force filed will be suitable for united atom (ac
Dear Gromacs users,
I am planing to do a protein simulation in acyl chain united-atom POPC
membrane model. It will of great help if few of my queries regarding
setting up the system get answered.
1. Which force filed will be suitable for united atom (acyl chain) POPC?
Will CHARMM36 have united at
