[gmx-users] Minimization Problem

Dear Gromacs community I am trying to run a simulation of choline molecule but found various errors concerning to bonds, angles and dihedrals during the minimization. Part of the top file (line number in the first column): ... 29 [ bonds ] 30; aiaj funct 311 4 1; N

Re: [gmx-users] Ionic liquid simulation problem

Hi Ghosh, Thanks for your answer. But I'm not sure if I understood what you meant. I already used insert-molecules command to create a box with the cationic species. Now, should I use the same command to include the anionic species into the box? Best *Prof. Dr. Ednilsom OrestesDepartamento de

[gmx-users] Fwd: Ionic liquid simulation problem.

* -- Forwarded message -- From: Ednilsom Orestes <eores...@gmail.com> Date: 2017-09-05 15:32 GMT-03:00 Subject: Ionic liquid simulation problem. To: gromacs.org_gmx-users@maillist.sys.kth.se Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an

[gmx-users] Ionic liquid simulation problem.

Dear GROMACS Community, I am very new with GROMACS I am trying to run a simulation of an ionic liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to the following protocol: 1. Prepared the respective PDB files and added/modified the OPLS/AA force field parameters updating