Hi, I forwarded your email to the GROMACS users list, please use it for user questions. In this way you have a greater chance of getting answers and others can find the questions and answers online.
>I have a 2 microsecond trajectory of protein-ligand system. I want to >calculate 3 things: > >1. Time series of number of water molecules in binding cavity. Give gmx select a try. You could select water molecules within a certain distance of atoms of cavity lining residues. >2. Volume evolution of in the binding cavity. There are a number of tools not distributed with GROMACS that you could try, for example trj_cavity htt<https://sourceforge.net/projects/trjcavity/>ps://sourceforge.net/projects/trjcavity/<https://sourceforge.net/projects/trjcavity/> and caver https://www.caver.cz >3. Water surface density evolution in the cavity. I'm not sure how you would define this quantity but a combination of the select and sasa tools of gmx may work. Best, Thomas. -- 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.
