Mark,
> 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. This can gain in terms of avoiding of time-consumptions solvation phase (e.g G_membeded takes addition 50ns of simulation time ) > 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? I've found in manual only nh-chain-length (10) parameter wich could be added to t_couple= Nose-Hoover. Does the introduction of that parameter turn on the different t_couple regime ? How I could chose the value ( from 1 to 10) of that parameter in case of simulation of mrmbrane proteins if I use SD integrator ( not MD). Does any other integrator could be most suitable for chains regime ? James -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
