[gmx-users] re-equilbrating membrane protein system after g_membed and ligand addition

Peter C. Lai pcl at uab.edu
Fri Jul 29 14:05:49 CEST 2011

I was looking at the g_membed paper recently, and noticed the authors "only"
spent 10ns to re-equilibrate the membedded-system after g_membeding.
This they also did after bumping the temperature from 300 to 323K "to prevent
ordering of the bilayer" even though the "typical" simulation temperatures of 
POPC is 300 to 310K...Anyone know why 323K was used? Was it to compare it
to the DOPC environment or something?

I noticed for my particular system, I had to run a round of EM on the 
post-membedded system in order to resolve some clashes before I could mdrun. 
Then I ran 10ns in NPT with gen_vel=yes at 310K and position restraints on 
the helix CA atoms. I am inferring that because the membrane patch I used had 
been previously equilibrated after I constructed it and ran it under NPT at 
300K for 100ns, 10ns should be sufficient time to re-equilibrate with the
protein in the middle and 310K temperature?

After the 10ns with protein restrained, I ran Grid_MAT on it and got a 
reasonable APL (61-62A^2/lipid when taking protein atoms into account,
comparable to pre-g_membed patch) and the box dimensions look stable. Is
this sufficient to answer the abvove question?

Now I am going to be introducing a ligand to the protein. Is there a way to 
preserve any state, like velocities of all the previous atoms? I was thinking
of the doing the EM while freezing everything but the ligand atoms and 
allowing the ligand to change conformation (like a docking refinement). After 
this, can I have the thermostat and barostat rescale the original velocities
(and gradually heat the ligand) instead of reinitialising everything?

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| BEC 257
Genetics, Div. of Research	| 1150 10th Avenue South
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

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