Thanks again for your response. I appreciate all your help. On Sat, Apr 23, 2011 at 6:11 PM, Fabian Casteblanco <fabian.castebla...@gmail.com> wrote: > Hello, > > I'm trying to fill a box with methanol using CHARMM FF Parameters. I > also need to do this for ethanol and 1-propanol. > > For ethanol, each individual molecule had approximately -19 kJ/mol of > potential energy, then I placed 1000 in a box, performed nvt, npt, > etc. End Result: A negative potential energy (it means that its > stable?) and a density of 0.785 g/cm3 compared to actual 0.789 g/cm3 > at 1 atm, 298 K. This result seemed ok. > > For methanol and 1-propanol, each individual molecule had a larger > 24 - 64 kJ/mol respectively, due to Coulomb 1,4 pair interactions (for > example, for methanol between the HA 0.09 and the H 0.43 gives a large > 64 kJ/mol). Again placed 1000 each in 2 separate boxes, performed > nvt,npt,etc on each one. End Result: A still positive potential > energy for each box (shouldn't this be negative after running npt? on > both) and a density that was 0.789 g/cm3 (for 1-propanol)compared to > actual 0.803 g/cm3 1-propanol at 1 atm, 298 K. Methanol density a bit > closer 0.787 compared to 0.791 g/cm3. > > My questions are: > -There should definetly be a positive potential energy after running > npt, correct? Otherwise it wouldn't be stable? I understand that the > 1,4 coulomb interactions should cancel out with nearby molecules. > *For CHARMM, they state that unless otherwise 1,4 parameters exist > already, they use a full scale 1.0 of the regular LJ, coulomb > potential. > > -As for the density, I know it's somewhat close but I'm trying to be > as accurate as possible. I read somewhere that the average cut-off > (rlist) is usually 1.4 for CHARMM and I had mine set to 1. I'm > guessing that having a larger cutoff would contribute more molecules > to the LJ, coulomb which might rise the density a bit to the correct > value? > > I'm still new to Gromacs so I appreciate all of anybodys help. Thanks a > bunch. > > -- > 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
