[gmx-users] gmxcheck and GROMOS96 bonds

Justin Lemkul jalemkul at vt.edu
Tue Jan 8 17:11:14 CET 2013

On 1/8/13 10:56 AM, Reid Van Lehn wrote:
> Hi Gromacs users,
> I was using gmxcheck to check a simple trajectory of surfactants, and get
> many errors of the type "Distance between atoms X and Y is 0.153, should be
> 0.023" where the actual distance is always approximately correct and the
> "correct" value is the square of the actual distance. This always occurs
> for G96 type bonds, where I am defining the bonds using the macros in the
> ffbonded.ff file for the gromos53a6.ff force field (e.g. gb_27 in that
> example). A typical line from my topology is then:
> [ bonds ]
> 3   4   2   gb_27
> etc.
> I also noticed the same errors when using gmxcheck on the output of the
> energy minimization in Justin Lemkul's KALP-15 tutorial, which also uses
> GROMOS96 bonds. I did not get errors for other steps in that tutorial,
> presumably because the bonds are constrained using LINCs.
> I am using Gromacs 4.5.5 and it appears that the relevant lines from the
> source code in gmxcheck.c are:
> switch (ftype) {
>      case F_BONDS:
>      case F_G96BONDS:
>        b0 = idef->iparams[type].harmonic.rA;
>        break;
>      case F_MORSE:
>        b0 = idef->iparams[type].morse.b0;
>        break;
>      case F_CUBICBONDS:
>        b0 = idef->iparams[type].cubic.b0;
>        break;
>      case F_CONSTR:
>        b0 = idef->iparams[type].constr.dA;
>        break;
>      default:
>        break;
>      }
> It's not clear to me why b0 would be squared here since the switch
> statement doesn't look to discriminate between function 1 and function 2
> bonds (if I interpret this correctly). Do you think I have something
> incorrectly defined in my topology, or does gmxcheck not correctly process
> G96 bonds? Since the actual bond lengths look correct I'm not too worried
> about it, but I want to resolve any errors if they do exist since right now
> gmxcheck cannot really be used to find actual bonding errors. I apologize
> if this is something obvious that I missed as I am a beginner in Gromacs.

This appears to be a small output bug.  There is nothing wrong with your 
topology or simulation.  Please file a bug report on redmine.gromacs.org with 
all of the information above.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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