[gmx-users] Does Non-Protein include SOL?

Justin Lemkul jalemkul at vt.edu
Tue May 10 23:00:25 CEST 2016

On 5/10/16 4:47 PM, Irem Altan wrote:
> Hi,
> I am simulating a box of TIP4P water (NVT). For the temperature coupling I have the following:
> ; Temperature coupling is on
> tcoupl          = V-rescale     ; modified Berendsen thermostat
> tc-grps         = SOL   ; two coupling groups - more accurate
> tau_t           = 0.1     ; time constant, in ps
> ref_t           = 277     ; reference temperature, one for each group, in K
> When I set tc-grps to Non-Protein, GROMACS complains that such a group does not exist. I’d have thought Non-Protein would include SOL. What does Non-Protein refer to exactly?

It would include SOL if there was also a Protein group.  Non-Protein is only 
relevant when there is also Protein.  In the case of pure water, SOL and System 
(and maybe Other) should all be equivalent.



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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