[gmx-users] lipid / -OH oscillation period
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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