VMD-L Mailing List

From: Win Liu (mdsimulate_at_gmail.com)
Date: Mon Apr 01 2013 - 23:23:15 CDT

Hi JC,
Sure. I create a gmail, username is benzenefftk_at_gmail.com, a folder in its
drive includes the bonded optimization files for benzene. Hope you can
figure what's wrong.

Thanks a lot!
Wenhao

On Mon, Apr 1, 2013 at 11:51 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> Can you make all your files available somewhere off-list? Including the
> fftk logs. I wrote the bonded optimization code, so I need to be aware of
> weird cases like this.
>
> On Apr 1, 2013, at 11:11 PM, Win Liu wrote:
>
> > Hi VMD developers,
> > For a simple test to develop the forcefield with benzene molecule. In
> pdb and psf, Since benzene only had one type of carbon and hydrogen, CA and
> HP respectively. So the initial parameter file is
> > ...
> > BONDS
> > !V(bond) = Kb(b - b0)**2
> > !
> > !Kb: kcal/mole/A**2
> > !b0: A
> > !
> > !atom type Kb b0
> > !
> > CA HP 0.000 0.000
> > CA CA 0.000 0.000
> >
> > ANGLES
> > !
> > !V(angle) = Ktheta(Theta - Theta0)**2
> > !
> > !V(Urey-Bradley) = Kub(S - S0)**2
> > !
> > !Ktheta: kcal/mole/rad**2
> > !Theta0: degrees
> > !Kub: kcal/mole/A**2 (Urey-Bradley)
> > !S0: A
> > !
> > !atom types Ktheta Theta0 Kub S0
> > !
> > !
> > CA CA HP 0.000 0.000
> > CA CA CA 0.000 0.000
> >
> > DIHEDRALS
> > !
> > !V(dihedral) = Kchi(1 + cos(n(chi) - delta))
> > !
> > !Kchi: kcal/mole
> > !n: multiplicity
> > !delta: degrees
> > !
> > !atom types Kchi n delta
> > !
> > CA CA CA CA 0.0000 1 0.00
> > HP CA CA CA 0.0000 1 0.00
> > HP CA CA HP 0.0000 1 0.00
> > ...
> > When I am doing the bond calculation to get bond and angle parameters, I
> went through the hess calculation in Gaussian and used fftk to get
> BondedCalc.log file, I found the parameter, angle {CA CA HP} 0.000 0.000
> Obviously, this is not right(while bond {CA CA}, bond {CA HP}, angle {CA CA
> CA} all give reasonable non-zero value.) it seems that the fftk do not get
> the information for this angle.
> > And when I l dealt with Scan torsion module, in Dihedrals to scan table,
> I can only see CA CA CA CA dihedral(like 10 0 2 4, 6 8 10 0 and so on) but
> no HP CA CA CA or HP CA CA HP dihedrals, but they should be included,
> right? In addition, in my fftk plugin, I can not use "Edit Entry" tab, is
> it the issue that need to be fixed for VMD windows version? I am using
> 1.9.2 alpha.
> >
> > Sorry for long email but just to clarify my problem. Thank you in
> advance!
> > Wenhao
>
>