VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 09:44:06 CDT

The mystery just turn worse! I ran in my laptop and I still obtain the same
values as before.... So it's not a problem with my cluster configuration,
at least it doesn't seems like.

2016-04-18 16:05 GMT+02:00 Laura Joana <laurajoanalopes_at_gmail.com>:

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