VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 09:05:44 CDT

I obtain close values, but they are not exactly equal:
NAMD
-7.75349182128906e+02 -7.74708642578125e+03 2.05269702148438e+03
-7.74688653758182e+02 -7.74826807202096e+03 2.05239478592227e+03
-7.74603393652299e+02 -7.74890428783011e+03 2.05105687624320e+03
-7.75804016113281e+02 -7.74978466796875e+03 2.05070825195312e+03
-7.77042909993649e+02 -7.74924461376854e+03 2.05071753160505e+03

VMD
{-775.3491821289063 -7747.08642578125 2052.697021484375}
{-774.6886596679688 -7748.26806640625 2052.394775390625}
{-774.6033935546875 -7748.904296875 2051.056884765625}
{-775.8040161132813 -7749.78466796875 2050.708251953125}
{-777.0429077148438 -7749.24462890625 2050.717529296875}

But it's strange to thing that this slightly difference will cause such a
big difference in the dihedral values... Do you think the problem is here?

2016-04-18 15:40 GMT+02:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:

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