VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 08:31:40 CDT

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