@ Justin, Excellent advice. Thank you! And for the equilibrium angle, what is the approximate range I can define it to be? Say target is 90 degrees, should I define maybe 130 and let it oscillate? I guess question is how far is too far off?
Thanks, On Oct 31, 2013, at 4:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/31/13 4:44 PM, Xu Dong Huang wrote: >> @ Justin, >> >> I did not define [angles] in the topology but I do have the angles result >> from All-atom run using OPLS forcefield. The reason for me not to include it >> in MARTINI forcefield topology is because I wanted to see if it will produce >> similar angle result of atom 1&2, 1&3 and 2&3 in martini water since the >> behavior of particle types I chose for my 3 atoms are well defined by martini >> at this point. My interest is to find for which force constant K value will >> the martini model match the all-atom model using OPLS. >> >> And you’re right, sorry, I got confused about the angles, there should only >> be 1. However, even the angle value I received doesn’t match the traditional >> all-atom result. >> >> What will happen if I define the [angles] part with the angles I received >> from traditional simulation? Because ultimately I am trying to find the k >> value parameter that will make the 3 particle display an angle similar to >> traditional run. >> > > If you define an equilibrium angle for 1-2-3, it will oscillate harmonically > around that value, with the distribution determined by the value of k. I > suspect that is how you can tune the parameters, by matching the > distributions produced in the two simulations rather than a single target > value, because with the angle defined in the topology, you're sort of > predetermining the outcome. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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
