[gmx-users] Calculating diffusion coefficient in three dimension

Wed Nov 13 06:20:49 CET 2013

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.

On Wed, Nov 13, 2013 at 12:58 AM, Thomas Piggot <t.piggot at 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
>> 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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>>>>
>>>
>>>
>>>
>>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036