Hi all, I am a beginner to GROMACS and MD simulations in general. I’m trying to model electroporation in a DPPC membrane but I am having issues with the energy minimization step. I am basing my approach on the one followed in Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html) but without the steps that use the KALP peptide. After I solvate my membrane, I am trying to run energy minimization, but my steps are moving much slower than normal and I get the error "Water molecule starting at atom 109448 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate.” When I looked this error up, I found that this suggested that I had a bad starting structure, possibly with atoms overlapping. Based on this, I assume this error originates when I solvate my membrane. I am currently using the spc216.gro model. Is this an issue with my water model or am I doing something else wrong?
Thank you all very much for the help! -- Abhijit Jassem School of Nuclear Engineering Purdue University abhijitjas...@gmail.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.
