On Dec 9, 2009, at 3:41 PM, Justin A. Lemkul wrote:
Henry Yang wrote:
Hi there,
Thanks for telling how to calculate the area per lipid. But at the
same time if I want to draw a plot of area per lipid vs time then
how can I proceed? Any gromacs tool comes out which I can use?
thanks
You can obviously plot the box dimensions as function of time as
suggested by Justin
and then multiply the X and Y component (if the membrane is in the xy
plan) and divide
by the number of lipid per leaflet ...
No. As I said in my previous message, you will have to come up with
some script (or use some other software) to multiply those box
vectors and divide by the # of lipids per leaflet. You can then
plot those derived data.
-Justin
Henry
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*Sent:* Tue, December 8, 2009 12:49:18 PM
*Subject:* Re: [gmx-users] gromacs..
Henry Ynag wrote:
> Hello everyone,
>
> I am quite new to gromacs. I would like to know how can I
calculate the area per lipid for my simulations. I am running
simulations with 128 DMPC lipid bilayer. I have the output of 30 ns
simulations. Also how can i make a graph with this output.
>
Plot the relevant box vectors from the .edr file (g_energy). You
then have to come up with your own way to multiply these values (to
get the total lateral area) and divide by the # of lipids per
leaflet. A simple Perl script should do the trick.
-Justin
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list [email protected] <mailto:[email protected]
>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected] <mailto:[email protected]
>.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
