On 26/07/2012 10:14 PM, James Starlight wrote:
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 )
Only if the apo form has room for you to cut and paste in all your
ligands... You'll have to equilibrate independently in each case, so you
don't gain anything by not creating the system from the beginning each time.
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 ?
Have you looked in the manual and read about the options and compared
the citations it makes to the citations of the algorithm you want to use?
Mark
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