[gmx-users] aligning MD system to a reference (to use correlation driven MD with an EM map)

Cédric Leyrat Cedric.Leyrat at igf.cnrs.fr
Sat Jun 22 00:03:14 CEST 2019

Dear all,

I'm trying to apply the CDMD approach (Igaev et al. 2019, 
https://elifesciences.org/articles/43542). So I have this protein in a 
detergent micelle which I 've setup for MD in GROMACS using CHARMM-GUI. 
I want to align the MD system (protein+detergent+water and ions) to a 
reference pdb that fits the EM map.

I tried to use gmx confrms, which does the job fine.

gmx confrms -one -f1 reference.pdb -f2 moving_MD_system.pdb

However, whenever I try energy minimization from the resulting MD 
system, I get a force of +inf.

Steepest Descents converged to machine precision in 16 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  1.1009935e+17
Maximum force     =            inf on atom 84639
Norm of force     =            inf

If I try to equilibrate the system I get this message:

Program:     gmx mdrun, version 2018.4
Source file: src/gromacs/mdlib/sim_util.cpp (line 776)
MPI rank:    1 (out of 42)

Fatal error:
Step 0: The total potential energy is 1.44323e+13, which is extremely high.
The LJ and electrostatic contributions to the energy are 1.44323e+13 and
-33602.8, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.

Could anyone please explain why this is happening and how to obtain an 
aligned MD system that can be simulated?

Thank you in advance,


Cédric LEYRAT, Ph.D
Chargé de recherche - INSERM
Institut de Génomique Fonctionnelle
141, rue de la cardonille
34094 Montpellier Cedex 05 - France
tel: +33 (0)434359272

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