[gmx-users] (no subject)

[Anton Feenstra]

Robert d'Rozario wrote:

> Hi
> 
> I have a mixed bilayer and I want to run a simulation but I do not know
> whether
> to temperature couple the two different lipids together and make them one
> group
> or to leave them seperate.
> 
> One of the lipids is neutral overall and the other has an overall charge
> of -1.
> I have added counter ions to make the whole system neutral.

In principle, one would want to couple the whole system to one bath.

In practice, different types of molecules, behave differently in energy 
(and thus temperature) drift, etc. This is not a problem so long as there 
is sufficient energy transfer possible between them. For, e.g., a protein 
in water this is not the case, which can get the protein to a different 
temperature than the solvent. Hence the need for different Tgroups. Also, 
for a bilayer vs. the solvent (water), I can imagine the energy transfer 
could be too low. But having two types of lipids mixed, even if one is 
neutral and the other charged, should not be a problem and I would suggest 
coupling them to one bath. The same if often done with counter-ions that 
are coupled to the same bath as the solvent. A ligand to a protein, on the 
other hand, could be coupled together with the protein.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|