[gmx-users] free energy calculation problem

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 8 13:05:23 CEST 2010

Павел Кудрявцев wrote:
> Hi,
> I wanna perform free energy calculation by changing parameters of
> amino acid residue. Since my case is rathe complicated first I tried
> to perform a very simplified task - to change only charges of atoms.
> So I peeked out one residue, keeped all its atom types and masses and
> changed charges of N and H atoms by +delta and -delta.
> After it grompp successfully genereted topology without any error or
> warning but when I run mdrun it terminates with following error
> Program mdrun_mpi, VERSION 4.5.1
> 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
> This error repeats even if I pick out another atoms not involved in
> improper dih. It seems like mdrun trying to perturb Improper Dih.
> which I don't wanna pertube at all. Could be there any simple solution
> or it's source code related?

The error does come from the source, but it's also easy to fix (and in fact, has 
been fixed in the git repository some time ago).  The solution is to add a line 
for F_IDIHS above F_PDIHS in src/gmxlib/topsort.c, i.e.:

     case F_G96ANGLES:
     case F_IDIHS:	/* this line is missing in 4.5.1 */
     case F_PIDIHS:
         bPert = (ip->harmonic.rA  != ip->harmonic.rB ||
                  ip->harmonic.krA != ip->harmonic.krB);

Then re-compile.


> I used following free energy options
> free_energy              = yes
> init_lambda              = 0.5
> delta_lambda             = 0
> I'd be very helpful for any advice,
> Pavel.


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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