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sphingomylein topology
- mandar
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5 years 7 months ago #7794
by mandar
sphingomylein topology was created by mandar
Hello,
I am new to the CG simulations of lipid bilayers and I have finished tutorial recently. I am planning to perform CG simulation of sphingomylein. However, I am confused which topology matches with sphingomylein molecule.
I think DPSM is closest to SM molecule.
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It will be really helpful if experts could comment and guide me in correct direction.
Thanks,
Mandar Kulkarni
I am new to the CG simulations of lipid bilayers and I have finished tutorial recently. I am planning to perform CG simulation of sphingomylein. However, I am confused which topology matches with sphingomylein molecule.
I think DPSM is closest to SM molecule.
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It will be really helpful if experts could comment and guide me in correct direction.
Thanks,
Mandar Kulkarni
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- bart
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5 years 7 months ago #7805
by bart
Replied by bart on topic sphingomylein topology
Sphingomyelin is not a single molecule, but a lipid class. Therefore using the right model comes down to which sphingomyelin you want to use. It is specified for each item in the lipid list which atomistic lipids they could/should represent. Keep in mind however, that the coarse grain lipid actually is an average of all the atomistic models it represents, with no tweaking of bond lengths towards a specific atomistic mapping.
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- mandar
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5 years 7 months ago #7806
by mandar
Replied by mandar on topic sphingomylein topology
Dear Bart,
Thanks for the previous explaination. I have used DPSM topology as we are working on N- palmitoyl-D-erythro-sphingosyl phosphorylcholine (d 18:1/16:0).
In case of DPSM, there are 2 topolgoies present and I found the following difference in the results of lipid bilayer thickness compared to experimental values.
1. Experimental thickness: 4.37 +/- 0.69 nm
2. New topology ( martini_v2.0_DPSM_01.itp): 3.95 +/- 0.05 nm
3. Old PPCS topology ( martini_v2.0_PPCS.itp): 4.16 +/- 0.06 nm
Please, if possible, I would like to request your opinion regarding my following assumptions:
1. The experimental SM molecule is (d 18:1/16:0) N- palmitoyl-D-erythro-sphingosyl phosphorylcholine. My guess is that due to 4:1 mapping I can still use DPSM topology provided on the website for this molecules. Is this a correct assumption?
2. Even though result for both topologies (DPSM and PPCS) are within standard deviation of experimental value, is it safe to assume that old PPCS topology better represent the current SM molecule?
3. If yes, Do we need to change D1B atom name to T1B in old PPCS topology, as the present double bond is trans double bond? However, as the atom type will remain C3, I hope the results will not change.
Thanks once again for the help. I look forward to further reply.
Thanks for the previous explaination. I have used DPSM topology as we are working on N- palmitoyl-D-erythro-sphingosyl phosphorylcholine (d 18:1/16:0).
In case of DPSM, there are 2 topolgoies present and I found the following difference in the results of lipid bilayer thickness compared to experimental values.
1. Experimental thickness: 4.37 +/- 0.69 nm
2. New topology ( martini_v2.0_DPSM_01.itp): 3.95 +/- 0.05 nm
3. Old PPCS topology ( martini_v2.0_PPCS.itp): 4.16 +/- 0.06 nm
Please, if possible, I would like to request your opinion regarding my following assumptions:
1. The experimental SM molecule is (d 18:1/16:0) N- palmitoyl-D-erythro-sphingosyl phosphorylcholine. My guess is that due to 4:1 mapping I can still use DPSM topology provided on the website for this molecules. Is this a correct assumption?
2. Even though result for both topologies (DPSM and PPCS) are within standard deviation of experimental value, is it safe to assume that old PPCS topology better represent the current SM molecule?
3. If yes, Do we need to change D1B atom name to T1B in old PPCS topology, as the present double bond is trans double bond? However, as the atom type will remain C3, I hope the results will not change.
Thanks once again for the help. I look forward to further reply.
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5 years 5 months ago #7935
by bart
Replied by bart on topic sphingomylein topology
Sorry for the late response I didn't see the follow up question. Usually we get mailed, but something must have gone wrong.
1) I think that the new mapping is probably better. If you would like to go for an older version, I think it is smart to read the involved articles and find out why the changes where made.
2) I think when things are within standard error it is not unwise to treat them as statistically the same.
3) I don't think I understand the question completely, but if the question is if you can change names in the topol file, then the answer is yes, you can do that. Do not change the type, for this will indeed change the behaviour.
1) I think that the new mapping is probably better. If you would like to go for an older version, I think it is smart to read the involved articles and find out why the changes where made.
2) I think when things are within standard error it is not unwise to treat them as statistically the same.
3) I don't think I understand the question completely, but if the question is if you can change names in the topol file, then the answer is yes, you can do that. Do not change the type, for this will indeed change the behaviour.
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- mandar
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5 years 3 months ago #7988
by mandar
Replied by mandar on topic sphingomylein topology
Dear Bart,
Thanks for your reply and sorry for late reply.
Actually, we have used new mapping for DPSM topology.
Thanks again.
Thanks for your reply and sorry for late reply.
Actually, we have used new mapping for DPSM topology.
Thanks again.
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