I guess the first parameter of each pair is easy to find. what about kb? k theta?..... kb is the force constant isnt it? any reference about a method how to calculate them please? pr anything atht might be of help.
Elie > Date: Thu, 4 Oct 2012 16:25:35 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] Error with "grompp" > > > > On 10/4/12 4:22 PM, Elie M wrote: > > > > I guess now I get what is happening finally. Correct me if I am wrong. The > > .top file was produced using an .n2t file (mine was ffoplsaamod.n2t) which > > was also modified to include atoms that were not there *but present in > > atomtypes.atp). The .top file describes all the bonds and angles in the > > molecule. This was successful. However the characteristics of some of those > > bonds are not described in the foplssabon.itp file; for example I have > > Sulfur > > in my molecule connected to carbon which has no entry in foplsaabon.itp and > > must be added to that file manually. I guess now I am in a position to check > > those bonds and add the relevant information which i will gather maybe from > > HYPERCHEM or ARGUSLAB??....A final question is in order here: what do the > > You will have to calculate reasonable values in some way, yes. > > > parameters (b0, kb), (th0, cth), (q0,cq), and (phi0, cp,mult) represent and > > in what units? > > > > All of this is in the manual. > > -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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
