[gmx-users] free energy calculation problem

Павел Кудрявцев pavkudr at gmail.com
Fri Oct 8 11:25:11 CEST 2010


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?

I used following free energy options
free_energy              = yes
init_lambda              = 0.5
delta_lambda             = 0

I'd be very helpful for any advice,

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