[gmx-users] Has anyone seen this error befor?

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 15 17:31:08 CEST 2010

TJ Mustard wrote:
> I started a small 2 nucleic acid system for FEP testing. As well as 
> turning on fep, I set RNA_Chain_A as the couple-moltype. I also set 
> couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then 
> began a "steep" mdrun and got this error:

Unrelated to your error, but potentially problematic: decoupling both LJ and 
Coulombic interactions simultaneously might lead to convergence problems.  See 
the free energy tutorial for information.

> Program mdrun, VERSION 4.5
> Source code file: topsort.c, line: 112
> Fatal error:
> Function type Improper Dih. not implemented in ip_pert
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> I have searched for this on google and found nothing. Do I need an 
> Improper Dihedral section in my top/itp file? I have ran this same 

If you have planar compounds (like nucleic acids), you likely have a [dihedrals] 
directive that corresponds to the impropers.  Check the function types.

> system with fep off and it runs perfectly.

It looks like the code in topsort.c does not deal with both F_IDIH and F_PIDIH, 
which maybe (?) is the source of the problem.  Normal harmonic impropers can be 
perturbed, i.e.:

     case F_IDIHS:
         bPert = (ip->harmonic.rA  != ip->harmonic.rB ||
                  ip->harmonic.krA != ip->harmonic.krB);

Perhaps there's something about your impropers that doesn't allow for 
perturbation.  At the very least, a test for F_PIDIH is missing, but I'll defer 
to the developers to weigh in on the need for a fix.


> Any help is much appreciated.
> TJ Mustard
> Email: mustardt at onid.orst.edu


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


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