[gmx-users] Temperature in CG production runs
jalemkul at vt.edu
Wed Oct 31 13:55:37 CET 2018
On 10/30/18 7:26 AM, Yasser Almeida Hernández wrote:
>> The reference temperature depends on what you want to model, and how
>> well the force field reproduces the phase transition temperature of the
>> lipids. If, for example, the force field requires higher temperature for
>> a lipid type to remain liquid crystalline than it should, you have to
>> decide if the higher temperature is reasonable or if you should be using
>> a different force field that is more accurate.
> What I want to model is the diffusion of several lipids, in
> interaction of a membrane protein. Buslaev and Gushchin
> (https://www.nature.com/articles/s41598-017-11761-5) simulated lipids
> at different temperatures using different FFs, showing little
> differences. In my case I have a bilayer with DPPE, DOPE, POPE, DPPG,
> DOPG, POPG and CDL, plus a membrane protein, so I think regular
> physiological 310K is the best, right?
That's your choice to make based on what you want to model. Offhand, it
seems reasonable, but don't plow ahead just because some guy on the
Internet said it's OK :) It's up to you to justify your choice based on
relevant, real-world conditions and how well the force field models what
you want it to under those conditions.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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