VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Apr 18 2016 - 08:40:03 CDT

Can you add the following colvar to your config, and then check its value
against the Cartesian coordinates of those atoms (you can get those in VMD):

colvar {
        name xyz
        cartesian {
                atoms {atomNumbers 5 7 9 15 17}
        }
}

Jerome

On 18 April 2016 at 15:31, Laura Joana <laurajoanalopes_at_gmail.com> wrote:

> Jerome,
> Does it help if I send you the output I'm obtaining with NAMD?
> Best,
> Laura
>
> 2016-04-18 15:24 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>
>> I just got the compiled version (linux x86_64) and I got the same wrong
>> values as before. I definitely cannot understand why I'm having this error!
>> It makes no sense....
>>
>> 2016-04-18 14:53 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>
>>> Actually I can try to use the compiled version for linux, the same as
>>> you, and see if my problem goes away...
>>>
>>> 2016-04-18 14:52 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:
>>>
>>>> I'm using the same version as you, NAMD 2.11 compiled from source in a
>>>> linux system, ethernet version! I cannot use the development version
>>>> because I got some problems with rattle in previous simulations....
>>>> Now this is so strange! Certainly there is something different in my
>>>> configuration that gives me that problem.... Any clue on how to find out
>>>> what?
>>>>
>>>> 2016-04-18 14:40 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:
>>>>
>>>>> 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/
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>