[gmx-users] Diffusion Cofficient of POPC

[Xavier Periole]

On Wed, 16 Jul 2008 07:18:17 +0200
  Jojart Balazs <jojartb at pharm.u-szeged.hu> wrote:
> Dear Minnale,
> As far as i know, at least 100ns simulation should be performed in order to 
> obtain the correct diffusion coefficient for lipids. I think, if you 
> performed 5 ns it is too short.
I am not sure about that! Probably depends on the lipid ... I would think
that with 10 ns you should be able to get a reasonable value.

The problem is I think that you have to restrict your fitting to the very
beginning of the msd curve. It looks like you are using the end of the curve.
>> # Diffusion constants fitted from time 500 to 4500 ps
This is typically where the uncertainty of the msd is the highest.

Look at the msd plot and restrict your fit to the first 100-200 ps or less.
The agreement should be much better.
> Hope this helps.
> balazs
> 
> minnale wrote:
>>
>>  
>> Hi all,
>>     I have read the literature about Diffusion cofficient(Dynamics in 
>> atomistic simulations of phospholipid membranes: Nuclear magnetic 
>> resonance relaxation rates and lateral diffusion, Vol-125, 
>> page-204703, Journal-THE JOURNAL OF CHEMICAL PHYSICS)
>> then I have given command like this
>> g_msd -f 5ns_popc.xtc -s .tpr -n p4.ndx -o msd_popc.xvg -lateral z
>> In the index file i have selceted p8 for the centre of mass and it 
>> will be  like this
>> [ P8 ]
>>   8  60  112  164 ......................
>>
>> I got the diffusion cofficient value like this
>> MSD gathered over 5000 ps with 501 restarts
>> # Diffusion constants fitted from time 500 to 4500 ps
>> # D[        P8] = 0.0131 (+/- 0.0190) (1e-5 cm^2/s)
>>
>> The actual D=(1-10)*10-7 cm2/s from above mentioned article but iam 
>> getting the value 1e-5 cm^2/s
>>
>> I have tried in different ways with options -type z but I didnt get 
>> the value near to actual value.
>>
>> Could you please tell me where I am doing mistake
>>
>> Thanks alot in advance.
>>
>>
>>
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-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------