[gmx-users] Simulation of the protein-ligand system embedded in membrane

James Starlight jmsstarlight at gmail.com
Thu Jul 26 14:14:52 CEST 2012

Dear Gromac's users!

I have some questions about simulation of the membrane protein
complexed with it's ligand in the membrane environment.

1- I want to simulate number of such similar systems ( e.g protein in
POPC bilayer) which differs only in ligand complexed into protein
interiour. Should I make my system from the biginning each time ? (
create protein-ligand complex in vacuu and make minimisation and than
do solvation in the POPC with further equilibration steps ) On other
hand if I know coordinates of my ligands in the protein interiour (
e.g from X-ray structures) is it possible to use apo-form of my
protein embedded in the membrane and place different ligands in that
protein-membrane complex? ( on other hand I dont want to do solvation
each time when I use new ligand )

2- I've found that the ussage of some thermostats could produce some
artifacts due to the energy distribution of T_coupl algorithms. In my
current protein-ligand system I want to use  Nose-Hoover's chains
thermostat. Does it  included in GROMACS ( I've found onlycommon
Nose-Hoover t_coupl algotithm) and what parametres of that chains
could be best suited for protein-ligand systems simulated in the npt
ensemble ?

Thanks for help,


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