VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 08:24:25 CDT

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