[gmx-users] Calculating diffusion coefficient in three dimension

[Venkat Reddy]

Thanks Justin. So, I have to calculate diffusion coefficient three times
(x,y,z) and finally add-up together to get in 3D???


On Tue, Nov 12, 2013 at 11:25 PM, Justin Lemkul <jalemkul at 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 <jalemkul at 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 <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.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at 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
>>>
>>> jalemkul at 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
>
> 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