Good morning, I am trying to run an umbrella sampling simulation, my system is a complex of two proteins. I have a couple of questions: 1. i don't know which is the purpose in defining the charge of each protein end 2. When i check the topol.itp file of the reference molecule i realized that it already has
#ifdef POSRES_B #include "posre_B.itp" #endif and when i check the file of the other protein it has it too 3. I don't know how to decide the size of the unit cell and which is the criterion to center the molecules 4. I am not sure why in the equilibration step and NVT it hasn't been done 5. In the neutralization part in this kind of simulation ones has to specified the concentration of the solution or i can do it just with the number of ions i want to add Thank you Paula -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
