@ 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. On Oct 31, 2013, at 4:26 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/31/13 4:22 PM, Xu Dong Huang wrote: >> @ Justin, >> >> That doesn’t sound very good. I tried it as he suggested using make_ndx, it >> seems to work, but it’s not reporting the result I want. When I use g_angle >> using the index i created, I chose the group I want to assess (My compound is >> very simple in Martini, it’s only represented by 3 atoms) and it reports back >> to me 1 angle value. However, I wish to assess the angle between atom 1 & 2, >> 2&3 and 1&3. How should I go about achieving that? >> > > If you have 3 atoms/particles, there can be only one angle, by definition. > > Do you have an [angles] directive in the topology? That's how mk_angndx > parses the .tpr file - by creating groups of similar angles based on theta > and ktheta. If your model doesn't specify any angle potential, then > mk_angndx will bail out and return nothing, though it should probably do that > in a more elegant way than producing an empty file. > > -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
