> Does that mean the atoms will shrink and adjust at the time inflategro step > and > this closely packed lipids will stay apart? Because as you said the energy > of course will be high on selected atoms during first EM step. > Could you suggest me that, can I proceed as such with my system, since there > is no problem in grompp and EM step (except high energy on some atom).
The energy will normalize during molecular dynamics stage. Dr. Vitaly Chaban > or Do I need to manually remove those overlapping lipids and water > molecules. > > Thanks in advance > -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
