[gmx-users] grompp warning

Qinghua Liao scorpio.liao at gmail.com
Thu Aug 10 10:23:51 CEST 2017

Hello GMX users,

I added another ligand as a new residue in the topology database, and 
then build the topology of the liand with pdb2gmx,
everything worked well. But I got this warning from grompp for a nvt 
equilibration after successful minimizations:

   There are atoms at both ends of an angle, connected by constraints and
   with masses that differ by more than a factor of 13. This means that
   there are likely dynamic modes that are only very weakly coupled. To
   ensure good equipartitioning, you need to either not use constraints on
   all bonds (but, if possible, only on bonds involving hydrogens) or use
   integrator = sd or decrease one or more tolerances:
   verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=
   4 or SHAKE tolerance <= 1e-05

It seems that there might be some problem of the topology file. But I 
can run grompp without any warning if I change the
constraints on all bonds to only bonds involving hydrogens. Then I ran a 
500 ps NVT equilibration, I checked the trajectory,
I did not found any wired angle. Could some one give me some tips? What 
is the possible reason that I got the warning?
Thanks a lot!

PS: to be consistent, I also need to apply constraints on all bonds.

All the best,

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