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, James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
