[gmx-users] Calculating diffusion coefficient in three dimension

[Justin Lemkul]

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 <vvchaban at gmail.com>wrote:
>
>> MSD is 3D by default.
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Tue, Nov 12, 2013 at 6:01 AM, Venkat Reddy <venkat4bt at 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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>
>
>

-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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