Hello Justin, I am running 2,000,000 time steps for the actual MD run (4,000 ps). Depending on how many solvent molecules I start with, I get slightly different results. Do you think its ok to run several different tests and take the average? Or perhaps take the end results of a shorter MD run and use those as the starting coordinates for a new run?
Thanks, Fabian -------------------------------------------------------- Fabian Casteblanco wrote: > Hello all, > > I'm running the same process from the free energy tutorial by Justin > Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html. > > How did the number of solvent particles get chosen (in the tutorial, 210 > molecules were chosen)? I seem to be getting slightly different If memory serves, I reproduced what was in the original paper, but do check. > results (ranging from as small as 200 J/mol to about 5 kJ/mol depending > on how many molecules I choose (ranging for example from 210 ethanol > molecules to about 610 ethanol molecules for the largest energy > difference change of about 5 kJ). I keep running tests to see if there > is some sort of minimum atom number to get steady consistent numbers but > I can't seem to find it. When I plot for example the bar.xvg & > barint.xvg for both sets to see where the lines don't match up, its > usually one or two points that differ slightly which cause the free > energies in the end to be slightly different. I seem to be noticing > too that the more atoms I use, the free energy gets a little bit lower. > > Does anybody have any experience with this? > How long are your simulations? I have experienced the case (using a water-octanol solvent mixture) where the initial configuration made a big difference in the result, so longer simulations and multiple configurations for the solvent were necessary to get reliable averages. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== On Thu, Jan 26, 2012 at 11:21 AM, Fabian Casteblanco <fabian.castebla...@gmail.com> wrote: > > Hello all, > > I'm running the same process from the free energy tutorial by Justin > Lemkul...http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html. > > How did the number of solvent particles get chosen (in the tutorial, 210 > molecules were chosen)? I seem to be getting slightly different results > (ranging from as small as 200 J/mol to about 5 kJ/mol depending on how many > molecules I choose (ranging for example from 210 ethanol molecules to about > 610 ethanol molecules for the largest energy difference change of about 5 > kJ). I keep running tests to see if there is some sort of minimum atom > number to get steady consistent numbers but I can't seem to find it. When I > plot for example the bar.xvg & barint.xvg for both sets to see where the > lines don't match up, its usually one or two points that differ slightly > which cause the free energies in the end to be slightly different. I seem > to be noticing too that the more atoms I use, the free energy gets a little > bit lower. > > Does anybody have any experience with this? > > Thanks. > > -- > Best regards, > > Fabian F. Casteblanco > Rutgers University -- > 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
