[gmx-users] CUT-OFFs for GROMOS96 43a1...Reg

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 31 14:22:04 CEST 2011

Kishore wrote:
> Dear All,
> I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) 
> with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 
> force field for the simulations. I need a clarification on the CUT-OFFs 
> applicable for this force field. I have seen many people using *rvdw = 
> 1.4* and* rcoulomb = 1.0 ( short range vander-waals and elctrostatics 
> cut-offs) *in all the .mdp files. In the tutorial I am following (Justin 
> Lemkul's - protein ligand complex)) he used *rvdw = 1.0* and *rcoulomb = 
> 1.0* in case of energy minimisation and* rvdw = 1.4* and *rcoulomb = 
> 0.9* in case of NVT/NPT equilibration and production MD run. So, someone 
> please clarify me what the widely accepted values for these two would 
> be. If at all I should use* rvdw = 1.4*, then should -d flag in editconf 

The latter.  EM is relatively insensitive to the cutoffs in my experience, so 
1.0 is fine there.  For the real MD, use the proper settings given in the 
production MD .mdp file.

> be atleast 1.4 or can it be less than that in the case of PBC conditions 
> enabled.

You simply have to ensure that your system's components never "see" one another. 
  In principle, you'd be safe setting -d 1.4 and have a maximum of 2.8 nm 
between periodic images.  That can result in a lot of wasted time doing 
calculations on distant water molecules when the box size gets extremely large. 
  If the box size/shape will not change much (as is the case for most 
well-equilibrated protein/water systems), you can get away with a shorter value 
of -d, maybe 1.0 or so.  Don't set it as low as 0.7 (such that the periodic 
distance is exactly 1.4 nm, equal to the cutoff), because then any small 
fluctuation can cause you problems.


> -- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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