Apologies, yes I meant to link to the paper you sent ("A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field").
Cheers,
Callum
________________________________
From: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Sent: Tuesday, January 24, 2017 10:41:32 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Simulating lipid bilayer below phase transition temperature
Hi,
thanks a lot for your help.
Yes, I confirm that my system is below phase transition temperature.
I will follow your advice, performing different simulations for different temperature values.
I had a look at the paper you mentioned. You mentioned twice the same paper. If I have understood correctly, I guess that the paper concerning validated parameters for cholesterol is this one:
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.5b04924
Thanks again!
Tommaso
________________________________________
Da: Dickson, Callum J [callum.dickson09.imperial.ac.uk]
Inviato: luned́ 23 gennaio 2017 23.37
A: amber.ambermd.org
Oggetto: Re: [AMBER] Simulating lipid bilayer below phase transition temperature
Hi,
Simulation of PC/Chol mixtures is possible using the recently derived parameters for cholesterol which have been validated in this paper:
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.6b01870
Phase behaviour of lipids using Lipid14 has not been extensively studied and melting points etc were not used as target data during derivation of the force field. A recent paper found that the melting point of DPPC using Lipid14 was somewhat over-estimated:
http://pubs.acs.org/doi/full/10.1021/acs.jpcb.6b01870
If I understand correctly, you would like to model a DPPC/Chol system in the gel phase (ie below the phase transition to liquid crystalline)?
I would suggest first running DPPC/Chol mixtures at different temperatures and ensure that it is in the correct phase that you wish to simulate, bearing in mind the melting point of the system may not match experiment.
Callum
________________________________
From: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Sent: Monday, January 23, 2017 5:12:24 PM
To: amber.ambermd.org
Subject: [AMBER] Simulating lipid bilayer below phase transition temperature
Dear Amber users and developers,
I need to simulate a DPPC/Cholesterol (85% DPPC 15% Cholesterol) lipid bilayer and its interactions with different drug molecules. For this purpose, I am using LIPID14 force field and GAFF force field.
According to the literature data, phase transition temperature is still higher than the value used in the experiments.
I would like to know if it is still possible to simulate this system. Indeed, although in the various tutorials the target temperature in the simulation was much higher than phase transition temperature, I found other examples where the situation was the opposite, like here:
http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/c5cp01937k#!divAbstracthttp://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/c5cp01937k#!divAbstract
Can you suggest me a proper simulation protocol and/or more literature references?
I thank you in advance for your help and collaboration.
With my best regards,
Tommaso Casalini
Post-doctoral fellow, ETH Zurich
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Received on Tue Jan 24 2017 - 11:30:03 PST
