[gmx-users] CHARMM36 and energygroup exclusions

Justin Lemkul jalemkul at vt.edu
Tue May 2 19:45:59 CEST 2017

On 5/2/17 1:34 PM, Daniel Bauer wrote:
> Hello,
> I need to run a simulation of a membrane system with CHARMM36 and
> energygrp exclusions. Therefore, I used the mdp settings suggested by
> the gromacs page but a lower rvdw-switch (0.8 instead of 1.0) to better
> reproduce DPPC lipid params:
> constraints = h-bonds
> cutoff-scheme = Group
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 0.8
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
> Since I need to exclude energy groups, I cannot use the Verlet cufoff
> scheme but have to use group scheme instead. However, It seems like this
> incompatible with the cutoff and rlist settings since I get a warning:
> WARNING 2 [file md0.mdp]:
>   The sum of the two largest charge group radii (19.291325) is larger than
>   rlist (1.200000)
> I think this is because rlist is the same size as rcoulomb and rvdw.
> However, setting a larger rlist is also not possible because of the PME
> coulombtype (Error: With coulombtype = PME, rcoulomb must be equal to
> rlist).

Your input configurations is probably broken across PBC, so grompp does a clunky 
calculation and thinks things are split really far apart.  It doesn't matter 
though, because CHARMM36 doesn't use charge groups.  Every atom is its own group 
so by definition you can't have any problems with this.


> My question is is it safe to ignore this warning if the simulation is
> only runs for a very limited time (2ns) or not? And if not, what changes
> to my settings would you suggest?
> To give you some background: I try to add a VdW sphere in my system that
> only interacts with the protein but allows water to pass through it
> freely (hence settin energygrp-excl between that particle and everything
> but the protein). After 2 ns, the sphere will be removed and the system
> can be simulated with the Verlet scheme and original settings again.
> Best regards,
> Daniel B


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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