From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Sat Apr 16 2016 - 07:34:20 CDT

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/
>>
>
>