[gmx-users] Calculating diffusion coefficient in three dimension

Venkat Reddy venkat4bt at gmail.com
Wed Nov 13 15:41:12 CET 2013 

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
) 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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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036

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