[gmx-users] Calculating diffusion coefficient in three dimension

Justin Lemkul jalemkul at vt.edu
Wed Nov 13 15:44:10 CET 2013 


On 11/13/13 9:41 AM, Venkat Reddy wrote:
> Dear Justin,
> I have referred to an article (Vuorela T, Catte A, Niemela PS, Hall A,
> Hyvonen MT, et al. (2010) Role of Lipids in Spheroidal High Density
> Lipoproteins. PLoS Comput Biol 6(10): e1000964.
> doi:10.1371/journal.pcbi.1000964), where the authors have clearly described
> the fitting of 2D diffusion coefficient to the surface lipids (diffusion
> along the lipid-water interface

Diffusion along a lipid-water interface is one thing.  Trying to use g_msd do to 
it is another, because I don't think it will.  It looks for a plane in the 
configuration and calculates relative to it.  I suspect you will need to modify 
the code to implement a custom algorithm.

-Justin

> ) and 3D diffusion coefficient to the core lipids.
>
>
> On Wed, Nov 13, 2013 at 7:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/13/13 12:20 AM, Venkat Reddy wrote:
>>
>>> 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.
>>>
>>>
>> 2D diffusion coefficients are what the -lateral option does.  I really
>> don't understand why you want a 2D value for anything with spherical
>> symmetry.  If there is an outer layer of a vesicle, that's as much a sphere
>> as anything inside it.
>>
>> -Justin
>>
>>
>>
>>> 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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>>>
>>>
>>>
>> --
>> ==================================================
>>
>> 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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