[gmx-users] Error with "grompp"

[Elie M]

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: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> 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
> 
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