normal Electrostatic Potential membrane pores

  • satti
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2 years 11 months ago #8906 by satti
Dear all,

I am interested in calculating the electrostatic potential of membrane pores in complex martini membranes (such as the Plasma membrane). For this, I tried the PMEPot plugin of VMD. The calculated potential maps show a min value of -25V and max as +18V. I am a bit suspicious of such high values.

Does anyone think that such values are possible. I would appreciate any comments as the calculation is part of the revision work of a paper.

kind regards,
satti

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2 years 11 months ago #8907 by vainikka
Replied by vainikka on topic Electrostatic Potential membrane pores
Disclaimer: Not an expert on the topic, nor on the tool.

Looks like PMEPot gives the result in units of kT/e, did you factor that in? Using that unit you would get a variation of ~1.1 V.

I'm sure there are previous works on the topic, where there's some discussion about the membrane potential of plasma membranes. A quick look on Google gives me a value of 100 mV, but you should definitely look this up yourself.

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2 years 11 months ago #8908 by satti
Replied by satti on topic Electrostatic Potential membrane pores
Dear Vainikka,

Thank you for looking into it and for your helpful comments.
Yes, I did use the conversion factor. One PMEpot unit of electrostatic potential is equivalent to 0.0258 Volts at 300K.

As you have mentioned that a quick look gives a value of ~100mV, this is what bothers me.

regards,
satti

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2 years 1 month ago #9326 by Junb
Replied by Junb on topic Electrostatic Potential membrane pores
Hi Satti,

I noticed that you use VMD to calculate electrostatic potential. I wonder how you can do it for MARTINI CG model. Could you kindly give me some help? I am a beginner of VMD and tried to use PME electrostatic plugin, and it always give me the same error of "no charged atom found". Thanks so much.

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2 years 1 month ago #9330 by xavier
Replied by xavier on topic Electrostatic Potential membrane pores
Hi,

The electric potential in VMD is determined/evaluated by the field generated by charges (partial) on the atoms.
In Martini that would correspond with the charges of the beads. They are determined manually when possible and required. The electric field obtained with VMD would be approximative and only indicative of appropriate at whole. Personally, I would be very cautious of the field obtained with Martini using VMD.

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2 years 1 month ago #9331 by Junb
Replied by Junb on topic Electrostatic Potential membrane pores
Hi Xavier,

Thank you so much for your prompt reply and helpful information.

May I please know how to use PME plugin to calculate the electrostatic field? Or could you please direct me to any tutorial of using it? I am facing the issue indicating "no charge of atom has been found" when I load CG pdb file. Many thanks.

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2 years 1 month ago - 2 years 1 month ago #9332 by xavier
Replied by xavier on topic Electrostatic Potential membrane pores
Hi,

I am sorry but I never calculated the electric potential with PME. Or I don’t remember. It might tricky to determine.

VMD or other software might be more informative.
Last edit: 2 years 1 month ago by xavier.

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2 years 1 month ago #9333 by Junb
Replied by Junb on topic Electrostatic Potential membrane pores
Okay. No problem. Thank you very much, I have already appreciated your kind information.

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