normal Electron density for Martini Membranes

  • ibrahim
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3 months 1 day ago #8316 by ibrahim
Hello All,
I am trying to compare the electron density profiles from Martini and all atom simulations of DOPC membranes to calculate Structure factor.
To calculate electron density using "gmx density" one has to supply an input file containing the number of electrons in each bead or atom. For all-atom system it is quite straight forward we know the number of electron for each atom. However for Martini beads it does not seem very straight forward. I assigned the number of electron to each bead as the sum of number of electron of all the atoms that maps into that bead. For example each water bead is assigned 40 electrons as 4 water molecules maps to one bead.
This way of electron assignment does not reproduce the electron density profile as seen in Atomistic simulations.
Here is the profile.
drive.google.com/file/d/1P6Y1V-90-xCfPVN...gz8/view?usp=sharing

I would highly appreciate for any suggestions regarding the assignment of electrons to martini beads.
Also Martini does not seem to reproduce the correct density for water, any feed back?.



Thanks
Ibrahim

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  • riccardo
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3 months 1 day ago #8317 by riccardo
Replied by riccardo on topic Electron density for Martini Membranes
Hi, I'm not really an expert on this so can't spot it right away; but, first of all, could you compute successfully the density profile in the tutorial ? cgmartini.nl/index.php/tutorials-general-introduction/bilayers

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3 months 1 day ago - 3 months 1 day ago #8318 by ibrahim
Replied by ibrahim on topic Electron density for Martini Membranes
Thanks for your response.

The tutorial does not mention how to assign number of electron to each bead. It only mentions the following
A more appropriate way to compare to experiment is to calculate the electron density profile. The g_density tool also provides this option. However, you need to supply the program with a data-file containing the number of electrons associated with each bead (option -ei electrons.dat). The format is described in the gromacs manual.
Last edit: 3 months 1 day ago by ibrahim.

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