# Re: [gmx-users] Calculating diffusion coefficient in three dimension

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On 11/12/13 12:30 PM, Venkat Reddy wrote:
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```Dear Sir, Thanks for the quick reply.
So, I have to declare -type no flag. Isn't it??
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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.
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```and I have recently gone through Justin's membrane protein tutorial, where
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You mean my tutorial :)

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```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.

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Yes, a representative atom is usually what is passed to g_msd.

-Justin

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On Tue, Nov 12, 2013 at 9:57 PM, Justin Lemkul <jalem...@vt.edu> wrote:

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On 11/12/13 11:25 AM, Venkat Reddy wrote:

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```Then, how to mention the direction for spherical particles Sir?

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```Read g_msd -h again, paying specific attention to the -type flag.

-Justin

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```On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul <jalem...@vt.edu> wrote:

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On 11/12/13 8:55 AM, Venkat Reddy wrote:

Thank you sir for the prompt reply.
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```*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
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```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

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```wrote:
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MSD is 3D by default.

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```

Dr. Vitaly V. Chaban

On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat...@gmail.com>
wrote:

Dear all,
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```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)?

--
With Best Wishes
Venkat Reddy Chirasani
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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