[gmx-users] gmxcheck and GROMOS96 bonds

[Reid Van Lehn]

Will do, thank you for fast response!

Reid

On Tue, Jan 8, 2013 at 11:11 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.orgwith all of the information above.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science