[gmx-users] lipid / -OH oscillation period

Justin Lemkul jalemkul at vt.edu
Mon May 8 14:08:25 CEST 2017

On 5/8/17 4:32 AM, Tamas Hegedus wrote:
> Hi,
> 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?

This is correct.  grompp finds H atoms by the first character in the atom name. 
Since yours are "1" instead of normal elemental symbols, it does not detect 1HO2 
as an H.  Adjust your atom naming, otherwise these will not be constrained.

> 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.

Identifying one problematic bond oscillation is enough to trigger the warning. 
So it will affect all equivalent interactions for the same reason.

> 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).

Changing the atom names, as indicated above, will solve this.


> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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