VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Apr 02 2013 - 07:39:32 CDT

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.