Hello, I'm trying to place 1000 molecules of 1-propanol using CHARMM FF parameters in a -box 6 6 6. After minimization, I realized that for a single molecule, the potential was slightly above 0, '+24 kJ/mol' to be exact, with electrostatic coloumb potential the greatest contributor. I used the same thing with OPLSA FF parameters and got a '+3 kJ/mol'. I realize that when I place 1000 of these molecules, the potential will be very high since the potentials are positive to begin with. When I placed 1000 molecules using:
- "genbox -ci propanol.gro -nmol 1000 -box 6 6 6 -o prop1000.gro" I resulted with a box full of 1000 molecules in that specific box size on gromacs 4.0.1. I did the same on the latest gromacs 4.5 but it ended up taking longer and the last line stating 'killed'. I redid it with a box 7 7 7 and it worked on gromacs 4.5. However, after I energy minimized both 1000 molecules (box 6 6 6 on gromacs 4.0.1) and (box 7 7 7 on gromacs 4.5), the first gave me a large negative potential energy (-6000 kJ/mol) after taking a long time and the second box gave me a somewhat large 2*10^3 kJ/mol. I am still new to Gromacs but I'm confused on why a certain box size worked on one version of gromacs and the other didnt. I assume that the difference in potential energies is since the 2nd box has way more space for these molecules therefore they are not as well equilibrated as the more compact box of size 6 6 6. Why does my box size that worked on gromacs4.0.1 work and on 4.5 it states killed as the last line and only works redoing it with a bigger box size. Thank you so much for your time and help ahead of time. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: fabian.castebla...@gmail.com -- 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
