Hi Venkat,
Can you make it a bit clearer what you actually want?
If it is the diffusion of the lipids along the curved surface of the
vesicle, rather than simply the overall 3D diffusion, this is not
trivial to calculate as I don't believe g_msd will do this for you. This
property has been studied before though, so I suggest you search the
literature for papers simulating vesicles to see how the lipid diffusion
was calculated.
Cheers
Tom
On 11/12/2013 06:35 PM, Justin Lemkul wrote:
On 11/12/13 1:33 PM, Venkat Reddy wrote:
Thanks Justin. So, I have to calculate diffusion coefficient three times
(x,y,z) and finally add-up together to get in 3D???
If you just want the overall diffusion constant, that's what g_msd
does without any additional options.
-Justin
On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/12/13 12:30 PM, Venkat Reddy wrote:
Dear Sir, Thanks for the quick reply.
So, I have to declare -type no flag. Isn't it??
The options for the -type flag are x, y, or z. You said you wanted the
diffusion coefficient in each spatial dimension. That is precisely
what
this option will do.
and I have recently gone through Justin's membrane protein
tutorial, where
You mean my tutorial :)
he has calculated diffusion coefficient for lipids in a membrane by
creating an index group for a particular atom. So, here also shall
I do
the
same thing? Moreover, mine is a coarse-grained system.
Yes, a representative atom is usually what is passed to g_msd.
-Justin
On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/12/13 11:25 AM, Venkat Reddy wrote:
Then, how to mention the direction for spherical particles Sir?
Read g_msd -h again, paying specific attention to the -type flag.
-Justin
On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 11/12/13 8:55 AM, Venkat Reddy wrote:
Thank you sir for the prompt reply.
*g_msd -f traj.xtc -s topol.tpr -n msd.ndx -lateral z -o
msd.xvg -tu
ns*
Here I am giving -lateral z (like for membrane simulations). Is it
fine
for
spherical systems also?
No. The system is a sphere, so what use is it to calculate
motion
perpendicular to z when you have lipids moving in all three spatial
dimensions? A vesicle is very different from a membrane, in
which the
lipids move in a plane, thus making "-lateral z" useful.
-Justin
On Tue, Nov 12, 2013 at 5:32 PM, Dr. Vitaly Chaban <
vvcha...@gmail.com
wrote:
MSD is 3D by default.
Dr. Vitaly V. Chaban
On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy
<venkat...@gmail.com>
wrote:
Dear all,
I am simulating a spherical lipid vesicle. I want to
calculate the
diffusion coefficient for each lipid component in 3D. How to
calculate
it
using g_msd (or any other tool like g_velacc)?
Thank you for your concern
--
With Best Wishes
Venkat Reddy Chirasani
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