Thank you Justin. Your explanation really helped. I was actually using 4.0.5, not 4.0.1 (my mistake). Your explanations explained everything very well. Thanks again for your help!
On Fri, Apr 15, 2011 at 3:33 PM, Fabian Casteblanco <fabian.castebla...@gmail.com> wrote: > 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 > -- 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
