Thanks Justin! I've updated the values accordingly. However can I ask where you found these? I'm curious if there is a site that I missed while searching.
Best, Parker On Fri, Jun 14, 2013 at 12:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/14/13 10:45 AM, Parker de Waal wrote: > > HI Maggin, > > > > The Pressure came from NPT simulation, I apologize for the lack of > > annotation. Here are some of the outputs of your suggested checks of > > equilibrium > > > https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing > > > > > > I'm currently looking into the rvdw value as you suggested as well as the > > fourierspacing as Mark suggested. > > > > However to help with this problem I've uploaded all of .mdp files as well > > as my bash script here -> > > https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902 > > Maybe there is a problem with my choice of box size? -bt cubic -d 1? > > Viewing the boxed and solvated system showed a distance of ~10A between > the > > protein and the box which should be ample. > > > > Additionally a full output log of the run can be found here -> > > http://research.parkerdewaal.com/slurm-940372.out > > which seems to be error free until the final md run. > > > > The cutoffs are wrong for 53A6. Standard usage: > > rcoulomb = 0.9 > rlist = 0.9 > rvdw = 1.4 > > The values of rcoulomb and rlist are fairly flexible when using PME. The > value > of rvdw generally should not be toyed with. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
