[gmx-users] Calculating diffusion coefficient in three dimension

[Justin Lemkul]

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 without 
any additional options.

-Justin

>
> 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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>
>
>

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

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

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