VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Apr 15 2016 - 11:50:32 CDT

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 <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, if you are measuring the dihedral of different atoms.
> Can you double check the atoms?
>
> Remember, the colvars atom numbers start with 1.
> In VMD, 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 <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
>>
>
>