GROMACS version: 2020.2
GROMACS modification: No
Is it possible to compute isothermal area compressibility in GROMACS directly?
I try to do it by computing that in excel, but I am not sure that everything is ok, so please check
To do that I get value box-x and box-y from gmx energy. and compute area per lipid X*Y/100 (my number of lipid in leaflet), so I have 0,70 nm^2 and standard error 0,01 nm^2
From there https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.6b01870
I take the mathematical formula to calculate isothermal area compressibility modulus
kB is the Boltzmann constant, T - the simulation temperature, ⟨AL⟩ the average area per lipid, and sAL the standard error of AL, nL number of lipids.
In my case
kB = 1.38064852 × 10-23 m2 kg s-2 K-1, but I have in nanometers my area per lipid so I change to
1.38064852 × 10-5 nm2 kg s-2 K-1 = 1.38064852 x 10-5 nm2 g s-2
T = 300K
= 0,69 nm^2 (69 A^2)
nL = 100 lipids (I have 100 lipid in one leaflet, my bilayer system consists of 200 lipids)
sAL = 0,01 nm^2
so:
2*1.38064852 × 10-5 nm^2 kg s^-2 K^-1 * 300 K * 0,7 nm^2
------------------------------------------------------------------------------- =
100 * (0,01 nm^2)^2
2*1.38064852 × 10-5 nm^2 kg s^-2 K^-1 * 300 K * 0,7 nm^2
------------------------------------------------------------------------------- =
100 * 0,0001 nm^4
After reduction
0,005796 kg s^-2
------------------------------------------------------------------------------- =
0,01
0,5796kg
------------- = but I must change to mNm^-1 like in article, so
s ^2
0,5796 kg * m
---------------------- =
s ^2 * m
0,5796 kg * m
---------------------- =
s ^2 * m
If:
N = kg * m * s^-2
so:
0,5796 N * m^ -1, but I must have mNm^-1, so 579,6 mN*m^-1
Do you think that is ok? Exp IACM is 180-330 for 298 K