Dear gmx users, Something very weird is happening with a .gro file and I wonder if any user has ever experienced something similar...
I am doing umbrella sampling simulation on a peptide with capped termini residues (ACE and NH2). As starting structure for the pulling simulations I used the last frame from a 150 ns simulation, in order to asses the stability of my system before the umbrella procedure. I did NVT and NPT equilibration, and then the MD run. Then I extracted the last frame of that 150 ns run and placed it into an appropriate box for the pulling, so I run again editconf, genbox and energy minimization. Then at the equilibration step the weird thing came: in the .gro file I have the ACE residues written as NH2 in one of the chains! The atom names remain as they have to according to the force field nomenclature (CH3, HH31, HH32, ...) for this ACE of this chain, but it is name as NH2!!! This is happening only in this .gro file at this step. Everything is fine in the first equilibrations, the MD run, the energy minimization in the newbox... It just shows up after this equilibration. I wonder if I may just change NH2 to ACE where it is to be or it has to be with something more complicated. -- gmx-users mailing list gmx-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
