[gmx-users] Problem in calculating static dielectric constant of Lysozymes
Suman Das
sumandas212 at gmail.com
Tue Nov 14 22:40:29 CET 2017
Thank you Prof. David for your reply and sorry for the late response. So,
now, do I have to use the original traj.xtc or still I need to do least
square fitting w.r.t the C-alpha atom and removal of translation/rotational
motion?
Thanks,
Suman
On 31/10/17 20:56, Suman Das wrote:
> > Dear Gromacs Users,
> >
>> I am trying to calculate static dielectric constant of Lysozymes using
> > gromacs version 4.6.7. I tried to follow the protocol used earlier by
van
>> Gunsteren (J. Phys. Chem. 1993, 97, 2009-2014). I used PME for the
> > electrostatic interaction. First, I converted the trajectory of protein
by
> > using the command 'trjconv -f traj.xtc -o protein.xtc -pbc whole -e
> > 1000.0". Then I removed the translational and rotational motion of the
> > protein w.r.t the C-alpha atom by the following command "trjconv -f
> > protein.xtc -o protein_fit.xtc -fit rot+trans". I choose C-alpha for the
> > least square fit. And finally g_dipoles command to calculate the
dielectric
> > constant "g_dipoles -f protein_fit.xtc -o Mtot.xvg -eps epsilon.xvg -a
> > aver.xvg -d dipdist.xvg -c dipcorr.xvg". However, the dielectric
constant
> > value (1.04) that I am getting is very less compared to the actual
> > dielectric constant (30).
> Since the proteins have a net charge you have to translate them to their
> center of charge such that the leading term Q/r in Eqn 1 in the paper
> disappears (in the paper they use center of mass which is not strictly
> the same but a good approximation). The problem is that trjconv does not
> do this and therefore your net dipole moment is incorrect (since it is
> origin dependent). A roundabout way to fix this would be to compute the
> center of mass with g_traj (gmx traj) and multiply that by the total
> charge of the protein and subtract that from the dipole components. The
> compute epsilon yourself.
>
>>
> > Dipole moment (Debye)
> > ---------------------
> > Average = 172.7138 Std. Dev. = 7.4113 Error = 0.0524
>>
> > The following averages for the complete trajectory have been calculated:
>>
> > Total < M_x > = 38.9789 Debye
>> Total < M_y > = 54.2911 Debye
> > Total < M_z > = -158.896 Debye
>>
>> Total < M_x^2 > = 1575.16 Debye^2
>> Total < M_y^2 > = 3006.62 Debye^2
>> Total < M_z^2 > = 25303.2 Debye^2
>>
> > Total < |M|^2 > = 29885 Debye^2
> > Total |< M >|^2 = 29714.9 Debye^2
>>
> > < |M|^2 > - |< M >|^2 = 170.091 Debye^2
>>
> > Finite system Kirkwood g factor G_k = 0.00570201
> > Infinite system Kirkwood g factor g_k = 0.00561463
>>
> > Epsilon = 1.04819
>>
> > Could you help me to find out what probably went wrong with the
calculation?
>>
>> Thanks,
>> Suman
>>
--
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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