Hi Agnivo, Temperature gradient means non-equilibrium MD (NEMD)
See notes from Prof. Martini: https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf What observable would you like to measure? Lets say you want to measure observable A. One "procedure" I can think of: 1. You can run all system at T=300K with NVT. After equilibrium, continue running all system at T=400K with freezing solvent group. See, to how to freeze a group, http://manual.gromacs.org/online/mdp_opt.html#neq To get a good statistic, you need to repeat this procedure K times as "solvent thermal wall" configuration would be different at each simulation. 100ps? Where did you get that? You need to see how observable A behaves to see if 100ps is enough, <A> time average. And see how <A> behaves in K different cases. 2. Similar to previous procedure but this time after freezing solvent group, run system in NVE. Again, you need to repeat this many times to get a good statistic. Similarly monitor observable A to see if 500ps is enough. However, I suggest you to talk to someone having NEMD experience as this procedure is just a heuristic approach. -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
