VMD-L Mailing List

From: Win Liu (mdsimulate_at_gmail.com)
Date: Tue Apr 02 2013 - 08:53:49 CDT

Hi people,
Sorry for the stupid thing I've done and I apologized for that. And I've
already change the password.

For Scan torsion part, I found my mistake, I click the Gui event on, so it
cover the "Edit Entry" tab and make me cannot use it, now it's ok. But for
Cal. Bonded part, I still get the angle {CA CA HP} 0.000 0.000 while the
other angle parameters looks reasonable, angle {CA CA CA} 20.65076666666667
120.00003333333332. Do you have some ideas about where I might wrong in
Cal. Bonded?

Wenhao

On Tue, Apr 2, 2013 at 8:39 AM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> This is a good point - what's to keep someone from replacing those files
> with virus-laden ones now? Please find a more appropriate way to share
> your
> data.
>
> That being said, it might save us some time if you would please run
> through
> the procedure again using the latest alpha version of VMD that you recently
> downloaded. I can't imagine that a bug of this magnitude escaped our
> attention, so it's quite possible that you made an error somewhere along
> the
> way.
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of
> Axel Kohlmeyer
> Sent: Tuesday, April 02, 2013 3:07 AM
> To: Win Liu
> Cc: JC Gumbart; Vmd l
> Subject: Re: vmd-l: Issue in Cal. Bonded and Scan Torsion in fftk
>
> On Tue, Apr 2, 2013 at 6:25 AM, Win Liu <mdsimulate_at_gmail.com> wrote:
> > And the password is mdsimulate. Sorry forget that.
>
> congratulations!!
>
> with this step (creating a bogus gmail account and publishing its password
> to a public mailing list) you will not only rank very high in the running
> for the "moron of the month" competition, but are also likely to violate
> several of usage agreement terms and - if reported to the proper places -
> risk corresponding penalties.
>
> worst of all, you helped to make life miserable for all regular users of
> gmail that will have to deal with further complications when using gmail in
> order to identify abuse like yours. :-(
>
> axel.
>
>
> > 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
> >>>
> >>
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International
> Centre for Theoretical Physics, Trieste. Italy.
>
>