[gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations. However, in your tutorial you set all charges to zero with the same settings in the mdp file. Can you please make this clear for me? Should I use the topoly file with the original charges for both calculations? Thank you, Sonia Aguilera Graduate Student-Chemical Engineering Department Universidad de los Andes Colombia -- View this message in context: http://gromacs.5086.n6.nabble.com/Topology-and-mdp-file-for-coupling-vdw-and-coulombic-interactions-for-running-FE-calculations-using-R-tp5001021p5001043.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
Re: [gmx-users] Re: Topology and mdp file for coupling vdw and coulombic interactions for running FE calculations using BAR
On 9/17/12 3:38 PM, Sonia Aguilera wrote: Hi Justin, So, are you saying that I should use my topoly file with all the original charges for both none-vdw and vdw-vdw-q calculations? I understand that the couple-lambda* setting dictate which parameters are involved in both calculations. However, in your tutorial you set all charges to zero with the same settings in the mdp file. Can you please make this clear for me? Should I use the topoly file with the original charges for both calculations? Yes, the topology can be complete with charges. They were zeroed out in the tutorial because (1) those were the files provided with an old Gromacs tutorial (for version 3.3.1) and (2) it was conceptually easier. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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