On Tue, 21 Mar 2017 13:09:46 +0530 abhisek Mondal <abhisek.m...@gmail.com> wrote:
> Hi, > > I just have a basic query. > > I'm working with a protein-ligand system with a goal of performing > Umbrella sampling in gromacs. So first, after I build the complex, I'm > going for NVT and followed by NPT equilibration of 20ns each. After > equilibration, is it mandatory that my equilibrated protein-ligand > complex matches exactly with the crystal structure used for > equlibration (I mean before and after) ? > > Please be comprehensive. I just need to understand something. It's easy to ask for a "comprehensive" answer on a mailing list but what you need to realise is that you are really asking about is the basics of molecular simulation. There is no quick answer to this and whole text books have been written on the topic. The way "equilibration" is typically used is to really mean to reach a nearby local minimum and expect to see a convergent behaviour with respect to a chosen target property. This paper, dx.doi.org/10.1021/acs.jctc.5b00784 may be an interesting starting point. You may also want to abandon words like "exact" or "correct" in this context. Cheers, Hannes. -- 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.