[AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system

From: carmine marco morgillo <FnTcy.hotmail.it>
Date: Wed, 30 Aug 2017 22:51:20 +0000

Dear Amber users,

I have performed a simulation of 150 ns. I want to calculate the lateral diffusion coefficient of the POPE molecules during a simulation on a protein in membrane. I found in the manual the stfcdiffusion command that may help to reach my goal, but I do not understand the whole syntax and the provided link to the code appears to be broken.

Using the Einstein relation (Brown, P. M.; Steers, J.; Hui, S. W.; Yeagle, P. L.; Silvius, J. R. Biochemistry 1986, 25,4259), valid at long times t:
2NDt = <|R(t) - R(0)|^2>

where D represents the lateral self-diffusion coefficient of the POPE molecules and is expressed in cm^2/s; the right hand of the equation refers to the mean square displacement (MSD) of an atom representative of POPE molecule (it may be considered as the center of mass of POPE, or simply the glycerol C2 atom); N is the number of torsional degrees of freedom considered (in my case I want to evaluate the displacement in xy plane, so I use N=2). t is the time of simulation (in my case 0.00000015 s).

I tried to calculated MSD using the command:

stfcdiffusion mask :PE.C2 xy out msd.dat

and I obtained a 5 column file like that:

        time x y z xy
     1.000 5399.016 4555.670 15219.316 9954.687
     2.000 5343.597 4557.516 15380.148 9901.113
     3.000 5251.178 4570.718 15249.222 9821.896
     4.000 5341.370 4563.900 15226.757 9905.269
     5.000 5345.501 4549.787 15221.376 9895.288
     6.000 5329.659 4511.651 15376.297 9841.310
     7.000 5290.646 4524.886 15396.781 9815.533
     8.000 5352.443 4487.592 15420.406 9840.035
     9.000 5380.037 4476.364 15379.228 9856.401
    10.000 5306.248 4452.621 15397.841 9758.869
Averaging the values of column#5 I would get the right hand of the Einstein equation (?).
I used that averaged MSD value to resolve the equation and derive D coefficient, but I get a very high value (1.5*10^9), whilst experimental value is about order of 10^-8

Please would you help me or correct me whether I am wrong on the interpretation of stfcdiffusion command.

Best Wishes,

Carmine Marco Morgillo, PhD
Dipartimento di Farmacia
FacoltÓ di Farmacia
UniversitÓ di Napoli "Federico II"
Via D. Montesano, 49
80131 Napoli
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Received on Wed Aug 30 2017 - 16:00:03 PDT
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