normal Electron density for Martini Membranes

  • ibrahim
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5 months 1 week 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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5 months 1 week 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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5 months 1 week ago - 5 months 1 week 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: 5 months 1 week ago by ibrahim.

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1 month 4 weeks ago #8418 by shakira
Replied by shakira on topic Electron density for Martini Membranes
Hi
In the case of lipid beads what should be the number of electrons to choose as the number of atoms in different beads are not an exact number rather than on an average terms. In this case what should be the number of electrons in the .dat file.

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1 month 3 weeks ago #8420 by riccardo
Replied by riccardo on topic Electron density for Martini Membranes
Sorry for the late reply. I see now that indeed in the tutorial it is not mentioned how to assign the electrons (by the way, this is the correct link for gromacs version > 5.x cgmartini.nl/index.php/tutorials-general...n-gmx5/bilayers-gmx5 ).

I don't know this from the top of my head but I would debug this in the following way: 1) find some references where they show data electron density profiles for Martini DPPC (you're using DPPC, right?) - for example, pubs.acs.org/doi/full/10.1021/acs.jpcb.6b00646 - and 2) see if you can reproduce the Martini data (for example, see Fig 5 of reference above); this includes separating the contributions to the density in heads, linkers, and tails, which will help debugging where the discrepancy comes from.
Actually, looking at Fig 5 of the reference above, it seems that Martini and CHARMM are in pretty good agreement. Your atomistic profile *seems* to be qualitatively different from the CHARMM one (but I'd rather wait for the figure with the contributions to give a decisive assessment).

Note than in the reference I linked they also have a polymer in there, which may perturb things a little. But this should give you a good starting point. Hope this helps.

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1 month 3 weeks ago #8425 by shakira
Replied by shakira on topic Electron density for Martini Membranes
Thanks for the reply. But still the question remains unanswered.
I m working with bilayer mixture which includes many types lipid molecules. If I calculate for a single lipid molecule the profiles shows erroneous peak heights. Still I didn't understand how to assign electrons for the beads. If it is like matching with the electron density profiles obtained previously on what basis will I assign the number of electrons. For example when I calculate for the PO4 bead I observed that the profiles matches well with the reference when I assign number of electrons as 470 instead of 47 (P = 15, 4 O = 32 = TOTAL 47 ). But what is the basis of this calculation. Will you kindly clarify my with this concern?

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1 month 3 weeks ago - 1 month 3 weeks ago #8426 by riccardo
Replied by riccardo on topic Electron density for Martini Membranes

shakira wrote: If it is like matching with the electron density profiles obtained previously on what basis will I assign the number of electrons.


That's not what I meant. I meant to try to reproduce a simple case, like DPPC, to understand the rationale behind making this electrons.dat files.

Your approach (PO4 corresponding to 47) sounds like the way to go. I don't see any reason why one would do it differently. So I don't understand why you'd need the factor of 10 larger number. I would really start from a simple case - instead of a mixture - and divide the density in contributions (PO4, tails, etc.) and compare to literature. I'm pretty confident that it should work with PO4 = 47 and similar.
In fact, to me your total Martini density drive.google.com/file/d/1P6Y1V-90-xCfPVNKJR5zIiWVccBomgz8/view doesn't look too far from the one reported, for example, here pubs.acs.org/doi/full/10.1021/acs.jpcb.6b00646 .

The discrepancy with respect to all-atom could also be due to the different resolution, i.e., more/less interdigitation of tails in the AA with respect to CG. Maybe what people do to compare to atomistic is that they map the atomistic bilayer to CG resolution and then compute the density in the mapped AA bilayer.
Last edit: 1 month 3 weeks ago by riccardo.

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1 month 3 weeks ago #8428 by shakira
Replied by shakira on topic Electron density for Martini Membranes
Dear Riccardo
Thanks for the detailed clarification. Well I was trying with the bilayer mixture rather than pure bilayer system. Let me try to reproduce with simpler systems firstly as suggested. If it didn't work perhaps reverse mapping can be a better option.

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1 month 3 weeks ago #8429 by shakira
Replied by shakira on topic Electron density for Martini Membranes
Dear Riccardo
Thanks for the detailed clarification. Well I was trying with the bilayer mixture rather than pure bilayer system. Let me try to reproduce with simpler systems firstly as suggested. If it didn't work perhaps reverse mapping can be a better option.

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