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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University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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