VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 07:53:44 CDT

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/
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>