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Definition of Q beads
- P_Banerjee
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5 years 9 months ago #7711
by P_Banerjee
Definition of Q beads was created by P_Banerjee
Hello MARTINI community,
I'm trying out the ultra-new MARTINI 3 version, but am not able to comprehend the definition of the newly introduced charged (Q) beads. It's not very clear from the included pdf. What do beads Qn, Qp mean? Negative and positive, eh?
Thanks.
Best,
Pallavi Banerjee
I'm trying out the ultra-new MARTINI 3 version, but am not able to comprehend the definition of the newly introduced charged (Q) beads. It's not very clear from the included pdf. What do beads Qn, Qp mean? Negative and positive, eh?
Thanks.
Best,
Pallavi Banerjee
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- paulocts
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5 years 9 months ago #7712
by paulocts
Replied by paulocts on topic Definition of Q beads
Hello Pallavi
Although you can find some examples of common usage for these Q-beads in the Summary_v3.0.b.3.2.pdf file, indeed we need a better description of in the documentation. Basically you have:
- Q2: divalent ions
- Q1: monovalent inorganic ions (like the phosphate in bilayers). Usually used for "hard" ions.
- Q0: monovalent soft ions. They could be organic (like choline group in a PC lipid) or inorganic (like BF4-).
-Qp/Qn: monovalent organic ions with positive (Qp) and negative (Qn) charges. the labels "n" and "p" give you different propensity for ion-pi interactions (which means different interactions with C1-C6 beads). These beads also have a bit more directionality than the other beads as Qp-Qp and Qn-Qn interactions are more repulsive.
You can use Q2, Q1 or Q0 as anions and cations, which is not the case of Qp/Qn. Do not forget that could try to use these beads in different sizes.
Don't be too attached to these names. We will probably change them in the near future. We are studying the possibility to add "p" and "n" labels for all the Q-beads (as all P- and N- beads can use "d" and "a"labels now).
Best,
Paulo
PS: We just found a typo in APPENDIX 3: propyl-ammonium should use Qp while propianate should be Qn.
Although you can find some examples of common usage for these Q-beads in the Summary_v3.0.b.3.2.pdf file, indeed we need a better description of in the documentation. Basically you have:
- Q2: divalent ions
- Q1: monovalent inorganic ions (like the phosphate in bilayers). Usually used for "hard" ions.
- Q0: monovalent soft ions. They could be organic (like choline group in a PC lipid) or inorganic (like BF4-).
-Qp/Qn: monovalent organic ions with positive (Qp) and negative (Qn) charges. the labels "n" and "p" give you different propensity for ion-pi interactions (which means different interactions with C1-C6 beads). These beads also have a bit more directionality than the other beads as Qp-Qp and Qn-Qn interactions are more repulsive.
You can use Q2, Q1 or Q0 as anions and cations, which is not the case of Qp/Qn. Do not forget that could try to use these beads in different sizes.
Don't be too attached to these names. We will probably change them in the near future. We are studying the possibility to add "p" and "n" labels for all the Q-beads (as all P- and N- beads can use "d" and "a"labels now).
Best,
Paulo
PS: We just found a typo in APPENDIX 3: propyl-ammonium should use Qp while propianate should be Qn.
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- P_Banerjee
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5 years 9 months ago #7715
by P_Banerjee
Replied by P_Banerjee on topic Definition of Q beads
Hi Paulo,
Thanks a heap for the explanation. I'll go ahead and play around then.
Best,
Pallavi
Thanks a heap for the explanation. I'll go ahead and play around then.
Best,
Pallavi
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