[gmx-users] lipid / -OH oscillation period

Tamas Hegedus tamas at hegelab.org
Mon May 8 10:40:25 CEST 2017


I have a protein/lipid system.
Using charmm36 ff and gromacs5.1.4.
I set constraints = h-bonds because of charmm.

1. After that grompp complains about the oscillation between an O and H 
in the lipid. Why? It should not.
Possible explanations I can imagine:
- does gromacs constrain only protein h-bonds?
- atom names are not recognized as an O-H?

2. Moreover, it complains only 1O2 1HO2 and not 1O3 1HO3. Why? It 
usually collect NOTEs upto a pretty large number of notes and I do not 
expect to stop after this one.

3. What can I do? What should I do? My system is large (~700,000 atoms), 
so I do not want to decrease the time step. I would like to increase it 
(use the standard 0.002 ps).

NOTE 2 [file topol.top, line 38]:
   The bond in molecule-type BDM between atoms 8 1O2 and 9 1HO2 has an
   estimated oscillational period of 9.1e-03 ps, which is less than 10 times
   the time step of 1.0e-03 ps.
   Maybe you forgot to change the constraints mdp option.

Thanks for your help and suggestion,

Tamas Hegedus, PhD
Senior Research Fellow
MTA-SE Molecular Biophysics Research Group
Hungarian Academy of Sciences  | phone: (36) 1-459 1500/60233
Semmelweis University          | fax:   (36) 1-266 6656
Tuzolto utca 37-47             | mailto:tamas at hegelab.org
Budapest, 1094, Hungary        | http://www.hegelab.org

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