wuxiao wrote: > Dear gmx users, > Usually, we perform NPT MD to achieve optimized density of system and > start another NVT MD to calculate other properties of interest. I think > there are three possible ways to choose the structure to start another > NVT MD:(1) the structure of last step in NPT MD trjectory;(2)the > structure in NPT MD trjectory with the density closest to the averaging > density;(3)the structure of last step in NPT MD trjectory but the box > size needs to be rescaled so that it is the averaging size. My question > is: which way should be chosen to start another NVT MD? I do not know > whether this question is suitable here. Any hints would be thanked very > much.
Bear in mind in your averaging that you're actually interested in the average *after* equilibration, which often does not include the start of a trajectory. Otherwise, I think it's largely irrelevant except that you don't want a density that's noticeably different from the one used in parameterization of the forcefield. You'll still need a period of further equilibration after any of the above choices. Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
