Dear All GMX Users I have some questions about doing NPT equilibration while keeping my protein (or small molecule) fixed. I know there have been a lot of discussion about this topic but after reading them I am still confused. So could anyone please give me some clear answer or insight about the following questions? Thank you in advance!!!
1) By including the pores.itp into my topology file, am I really position restraining the chosen atoms? I did a NVT equilibration with a pores.itp included in my topology file and "define = -DPOSRES" written in my .mdp file. After the mdrun was done, I used g_traj to check the coordinates of those "fixed" atoms. However, instead of seeing non-changed coordinates, I can see the Cartesian coordinates of those "fixed" atoms changed. The magnitude of changing is in the order of 0.001nm. 2) So if including pores.itp is not a good option for fixing chosen atoms, what is the best way to do it. What will the .mdp file look like? What I am really trying to do here is simply just to equilibrate my solvent molecule while keeping my protein (or small molecule ) fixed. Again, thank you in advance! -- View this message in context: http://gromacs.5086.x6.nabble.com/Position-Restraints-with-NVT-and-NPT-tp5015953.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.