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

```
On 11/13/13 9:41 AM, Venkat Reddy wrote:
```
```Dear Justin,
I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
Lipoproteins. PLoS Comput Biol 6(10): e1000964.
doi:10.1371/journal.pcbi.1000964), where the authors have clearly described
the fitting of 2D diffusion coefficient to the surface lipids (diffusion
along the lipid-water interface
```
```
```
Diffusion along a lipid-water interface is one thing. Trying to use g_msd do to it is another, because I don't think it will. It looks for a plane in the configuration and calculates relative to it. I suspect you will need to modify the code to implement a custom algorithm.
```
-Justin

```
```) and 3D diffusion coefficient to the core lipids.

On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul <jalem...@vt.edu> wrote:

```
```

On 11/13/13 12:20 AM, Venkat Reddy wrote:

```
```Dear Justin and Piggot,
Thanks for the suggestions. Actually, I have constructed a CG lipid
vesicle
by placing lipids in random conformation in a simulation box. My lipid
system is heterogeneous, i.e., it has different types of lipids
(POPC,CHOLESTEROL,PPC...etc). Some of them occupy the outer layer of
vesicle (POPC), and some stay in the intermediate region (CHOL). So, I
want
to calculate the diffusion rates of these lipids. Since POPC forms the
surface (polar heads interacting with water and their tails points to the
core), I suppose we have to calculate 2D diffusion for POPC. For the
lipids
in the core, they can diffuse in 3-dimension. So, it requires a 3D
diffusion coefficient for these core lipids. How to calculate 2D and 3D
diffusion coeff.? Hope I am clear.

```
```2D diffusion coefficients are what the -lateral option does.  I really
don't understand why you want a 2D value for anything with spherical
symmetry.  If there is an outer layer of a vesicle, that's as much a sphere
as anything inside it.

-Justin

```
```On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot <t.pig...@soton.ac.uk
```
```wrote:
```
```
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

-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)?

--
With Best Wishes
Venkat Reddy Chirasani
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!

* Please don't post (un)subscribe requests to the list.
```
```Use the

www interface or send it to gmx-users-requ...@gromacs.org.

```
```* Can't post? Read http://www.gromacs.org/
Support/Mailing_Lists

--

gmx-users mailing list    gmx-users@gromacs.org

```
```http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.

--
```
```
==================================================

```
```
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

==================================================

--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www
interface or send it to gmx-users-requ...@gromacs.org.

```
```    --

==================================================
```
```
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

==================================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.

```
```
--

```
```==================================================

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

==================================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.

```
```

```
```  --
```
```Dr Thomas Piggot
University of Southampton, UK.

--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.

```
```

```
```--
==================================================

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

==================================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/
Support/Mailing_Lists/Search before posting!

* Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.

```
```

```
```
--
==================================================

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

==================================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
```
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
```* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
```