Hi,
I want to calculate order parameter for POPC lipid.
After reading the comments made by Justin and Chris about g_order, i would like
to compare my results from both g_order and vmd tcl script which will compute
order parameters from real hydrogen atoms.
Below is the link I found for vmd
...@utoronto.ca]
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] order parameter
Dear Ramya:
Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your description of
what you have done (g_order
-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca]
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] order parameter
Dear Ramya:
Are you simulating all-atom lipids (with explicit hydrogen atoms
of chris.neale at utoronto.ca [chris.neale at
utoronto.ca]
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] order parameter
Dear Ramya:
Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca]
Sent: Thursday, September 01, 2011 1:35 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] order parameter
In addition to Justin's comment about g_order being incorrect
-users-boun...@gromacs.org] on
behalf of chris.ne...@utoronto.ca [chris.ne...@utoronto.ca]
Sent: Thursday, September 01, 2011 1:35 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] order parameter
In addition to Justin's comment about g_order being incorrect for
unsaturated carbons, you won't ever get
: [gmx-users] order parameter
Parthasarathi, Ramya wrote:
Hi Justin,
Thanks for the reply, and this is the graph, the red curve is what
GROMACS gives, the blue curve is what I get.. yes I am considering the
unsaturated carbons in to account. I have to see which is closer to the
experimental result
Hi,
I am trying to write a code for Deuterium order parameter of DOPC lipid. I went
through the code in gmx_order.c, I did the following,
1. I took the carbons in the chain, and found its neighbors.
2. Took the bilayer normal and found the angle between the bilayer normal
and the
Dear Ramya:
Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your description of
what you have done (g_order, for example, ignores explicit hydrogen
atoms so that it can act on united atom lipids).
Not sure why PBC
Sarah,
I remember some changes to the double bond awhile back, perhaps you're
using those?
POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe
someone has a reference for the updates.
Tim Sirk
--
gmx-users mailing listgmx-users@gromacs.org
Sarah,
I remember some changes to the double bond awhile back, perhaps you're
using those?
POPC (Berger/Tielman) is normally 'smoother' as Justin says. Maybe
someone has a reference for the updates.
Tim Sirk
--
gmx-users mailing listgmx-users@gromacs.org
Dear gmx users,
I am sorry to ask this question again, but reading in the email achieve did not
enlighten me. I found this email which describes my problem, but unfortunately
it has no replies:
http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html
Also there are these two
Sarah Witzke wrote:
Dear gmx users,
I am sorry to ask this question again, but reading in the email achieve did not
enlighten me. I found this email which describes my problem, but unfortunately
it has no replies:
http://lists.gromacs.org/pipermail/gmx-users/2008-July/034950.html
Fra: gmx-users-boun...@gromacs.org på vegne af Justin A. Lemkul
Sendt: to 25-02-2010 14:42
Til: Discussion list for GROMACS users
Emne: Re: [gmx-users] Order parameter for unsaturated lipid chain in UAmodel
Sarah Witzke wrote:
Dear gmx users,
I am sorry to ask
the literature - there's lots out there!
-Justin
Fra: Justin A. Lemkul [mailto:jalem...@vt.edu] Sendt: to 25-02-2010 15:14
Til: Sarah Witzke Emne: Re: SV: [gmx-users] Order parameter for unsaturated
lipid chain in UAmodel
Sarah Witzke wrote:
Thank you
Hi all,
i used united the atom force field model for the membrane lipids . to
calculate order parameter i used :
g_order -od -d
i know united atom force field doesn't have hydrogen atoms in hydrocarbons
chains .
i want to know gromacs calculates order parameter * Sc-c* or
*Sc-d*(Deuterium)
afsaneh maleki wrote:
Hi all,
i used united the atom force field model for the membrane lipids . to
calculate order parameter i used :
g_order -od -d
i know united atom force field doesn't have hydrogen atoms in
hydrocarbons chains .
i want to know gromacs calculates order
afsaneh maleki wrote:
thanks for your reply
i have got output file,i used the following options:
# g_order -f md.xtc -s md.tpr -n sn1.ndx -o order-sn1.xvg -od
deuter-sn1.xvg-d z
whatever deuter-sn1.xvg get me is the same Sc-c (the vector Ci-1,Ci,Ci+1
is considered as molecule
Hi,
I want to obtain order parameter for unsaturated carbons (eg. 9, 10) on
oleoyl (18 carbons) chains.
i use -Scd= 2/3 Sxx +1/3 Syy for the saturated carbons.
I try to calculate order parameters for unsaturated carbons, which is
defined as:
Scd=1/4Szz + 3/4 Syy + sdr(3)/2 Syz , with ignore
afsaneh maleki wrote:
Hi,
I am working on protein membrane that the lipid have one the
_unsaturated _bond on C9-C10.The force Field used is _united atom_.
I have some questions.
1- Is Sc-c (order parameter) valid for this lipid that contains the
unsaturated bond?
Please see the -unsat
Hi All !
Can anyone help me to find the order parameter of cholesterol as a
function of distance form the bilayer. I am doing a Lipid bilayer
simulation with POPC and Cholesterol.
Thanks a lot in advance.
Kushal Seth
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