VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 09 2013 - 10:28:43 CDT

Hi,
  I've posted a Win32 test build in the VMD alpha area on BioFS:
http://www.ks.uiuc.edu/Research/vmd/alpha/

This should incorporate the latest ffTK improvements, but I haven't
had a chance to check it very thoroughly yet. This build is the non-CUDA
version. I'm fixing a problem with one of our other Win32 build machines
and I expect to have a CUDA-enabled build posted as well.
Give it a try and let us know if you have problems with the new test build.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 08, 2013 at 07:08:44PM -0400, Wenhao Liu wrote:
> Hi John,
> Just for asking, when will the new windows vmd test build available, is it
> possible this week?
> Best
> Wenhao
> On Wed, Apr 3, 2013 at 4:14 PM, Win Liu <mdsimulate_at_gmail.com> wrote:
>
> Thank you so much for the information.
> Best
> Wenhao
>
> On Tue, Apr 2, 2013 at 3:50 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I will try to get a new Windows test build posted this week,
> including
> the latest ffTK code etc.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Tue, Apr 02, 2013 at 12:50:07PM -0500, Christopher Mayne wrote:
> > Wenhao,
> > As I thought, you are generating the BondedCalc.log file using an
> older
> > version of ffTK. What version of VMD are you using,
> specifically?
> > Probably the vmd192a13win32*.msi from alpha/old directory of
> BioCoRE?
> > More recent versions have an entirely new tab entitled "Opt.
> Bonded" that
> > is used for optimizing the bonded terms.
> > John, can you post a more recent Windows build to BioCoRE?
> > Regards,
> > Chris
> > On Apr 2, 2013, at 11:11 AM, Win Liu wrote:
> >
> > Hi Chris,
> > I've fixed the Edit Entry section missing problem, it is
> because I let
> > the Gui event on and it make the space for Edit Entry section
> too small
> > to show up, and when I set the Edit Entry off, I can see and
> use the
> > Edit Entry section.
> > The BondedCal.log and initialized parameter file are attached
> in this
> > email and also the output file from Gaussian calculation, hope
> you can
> > figure out where I am wrong. Thank you so much!
> > Wenhao
> >
> > On Tue, Apr 2, 2013 at 10:30 AM, Christopher Mayne
> <mayne_at_ks.uiuc.edu>
> > wrote:
> >
> > Wenhao,
> >
> > Based on the screenshot you attached, the Edit Entry section
> is indeed
> > missing. Potentially silly fix--have you tried resizing the
> ffTK
> > window to be taller? If that doesn't work, what version of
> Windows
> > are you running on?
> >
> > With regard to updating the parameters, if you find a less
> vulnerable
> > method for sharing the files, I'll take a look. A reasonable
> place to
> > start is to email me directly (off list) with your
> BondedCalc.log and
> > initialized parameter file; they shouldn't be very large, for
> which an
> > email attachment is appropriate.
> >
> > Regards,
> > Christopher Mayne
> >
> > On Apr 2, 2013, at 7:39 AM, JC Gumbart 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.
> > >
> >
> > <Ben_parm.prm><Benhess.out><BondedCalc.log>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/