[gmx-users] Calculating diffusion coefficient in three dimension

[Venkat Reddy]

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


On Tue, Nov 12, 2013 at 7:28 PM, Justin Lemkul <jalemkul at 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 <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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036