VMD-L Mailing List

From: Laura Joana (laurajoanalopes_at_gmail.com)
Date: Mon Apr 18 2016 - 07:52:01 CDT

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