From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Apr 18 2016 - 07:40:59 CDT

Yes, the VMD values are correct. I get the very same values with NAMD 2.11
and the current development version in Linux x86_64. What version and
system are you using?

Jerome

On 18 April 2016 at 14:36, Laura Joana <laurajoanalopes_at_gmail.com> wrote:

> Hi Jerome,
>
> Both commands gave me the same values and it seems the values I'm
> obtaining in VMD are correct because I'm also calculation then with measure
> and they are all the same! Now the problem is with NAMD...
> Are you obtaining -8.10195434545963e+01 and 7.02575414592844e+01 when
> running the file init.conf that I sent you? What version of NAMD are you
> using?
> Best,
>
> Laura
>
> 2016-04-18 14:20 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>
>> Hi Laura,
>>
>> Not sure what is happening, I cannot reproduce this problem. Can you
>> compare with large values of the box sizes? eg.
>>
>> molinfo top set {a b c} {0 0 0}; cv update; cv printframe
>> molinfo top set {a b c} {100 100 100}; cv update; cv printframe
>>
>> Best,
>> Jerome
>>
>> On 16 April 2016 at 14:34, Laura Joana <laurajoanalopes_at_gmail.com> wrote:
>>
>>> Hello Jerome!
>>>
>>> I tried to use the command line you gave me, but I still have different
>>> values for VMD and NAMD. With VMD I get:
>>> colvar -8.10195434545963e+01 7.02575414592844e+01
>>> and with NAMD I get:
>>> colvar -8.42715396480484e+01 5.74396799966552e+01
>>> Do you have any clue? And did you obtained the same values with the
>>> files I sent you? Because if you did it may be a problem with the versions
>>> of VMD and/or NAMD I'm using.
>>> Best,
>>>
>>> Laura
>>>
>>> 2016-04-16 12:16 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>>
>>>> Thanks Jerome! If that solves my problem I'll always going to include
>>>> that command line in my script when no periodic box information is given.
>>>> Best,
>>>> Laura
>>>>
>>>> 2016-04-15 19:22 GMT+02:00 John Stone <johns_at_ks.uiuc.edu>:
>>>>
>>>>> Hi,
>>>>> A very minor correction. Current VMD versions do set the periodic
>>>>> cell
>>>>> sizes to zero by default. That being said, there likely may still
>>>>> exist a
>>>>> molfile plugin or two that may be setting the periodic cell size to
>>>>> a non-zero number by default.
>>>>> Another possibility is that you may have loaded a file that had been
>>>>> processed
>>>>> by an old version of VMD that indeed did exactly what Jerome is
>>>>> warning about.
>>>>>
>>>>> Cheers,
>>>>> John
>>>>>
>>>>> On Fri, Apr 15, 2016 at 06:50:32PM +0200, Jérôme Hénin wrote:
>>>>> > Hi Laura,
>>>>> > The problem comes from a very unfortunate default behavior of
>>>>> VMD: when no
>>>>> > periodic box information is provided in a DCD file, it sets the
>>>>> box sizes
>>>>> > to 1, which breaks PBC-aware codes like colvars.
>>>>> > You can set them to zero with
>>>>> > molinfo top set {a b c} {0 0 0}
>>>>> > then the dihedral values are correct.
>>>>> > Best,
>>>>> > Jerome
>>>>> > On 15 April 2016 at 16:50, Karteek Kumar <[1]
>>>>> karthik3327_at_gmail.com> wrote:
>>>>> >
>>>>> > Hi,
>>>>> > The dihedral value of same four atoms should be equal either you
>>>>> > calculate using colvars or VMD.
>>>>> > How much different the values are?
>>>>> > I am afraid, A if you are measuring the dihedral of different
>>>>> atoms.A
>>>>> > Can you double check the atoms?A
>>>>> > Remember, the colvarsA atom numbers start with 1.
>>>>> > In VMD, A serial starts with 1 and index starts with 0.
>>>>> > Hope it helps !!!
>>>>> > Thanks
>>>>> > Karteek
>>>>> > On Fri, Apr 15, 2016 at 7:49 PM, Laura Joana
>>>>> > <[2]laurajoanalopes_at_gmail.com> wrote:
>>>>> >
>>>>> > Dear all,
>>>>> >
>>>>> > I'm having a problem with colvars module. I have a dcd file
>>>>> with just
>>>>> > one frame. I wrote a script to run in VMD and get two
>>>>> dihedral angles
>>>>> > using colvars module. So I have a colvars configuration file
>>>>> that
>>>>> > defines the groups to calculate the dihedrals like I normally
>>>>> need.
>>>>> > Everything works fine.
>>>>> > Then I made a config file for NAMD that only reads the same
>>>>> dcd file
>>>>> > and make "run 0". Then, using the same colvars configuration
>>>>> file, I
>>>>> > print the dihedral angles.
>>>>> > I supposed I would obtain the same values, as I just ran zero
>>>>> steps
>>>>> > before, but that is not the case. I'm obtaining different
>>>>> values! Can
>>>>> > someone explain me why? Or, has someone here already had the
>>>>> same
>>>>> > problem.
>>>>> > My system is just the di-alanine molecule in vacuum.
>>>>> > Thanks,
>>>>> >
>>>>> > Laura
>>>>> >
>>>>> > References
>>>>> >
>>>>> > Visible links
>>>>> > 1. mailto:karthik3327_at_gmail.com
>>>>> > 2. mailto:laurajoanalopes_at_gmail.com
>>>>>
>>>>> --
>>>>> 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/
>>>>>
>>>>
>>>>
>>>
>>
>