VMD-L Mailing List

From: Win Liu (mdsimulate_at_gmail.com)
Date: Mon Apr 01 2013 - 23:25:12 CDT

And the password is mdsimulate. Sorry forget that.

On Tue, Apr 2, 2013 at 12:23 AM, Win Liu <mdsimulate_at_gmail.com> wrote:

> 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
>>
>>
>