[gmx-users] Simulation box size, LIE and PME

[Justin Lemkul]

On 11/8/13 2:27 PM, Williams Ernesto Miranda Delgado wrote:
> Greetings
> The discussion list had helped me about understanding what to do when I
> want to calculate binding free energy using LIE after doing MD simulation
> using PME.
> Now I need your help about choosing the simulation box size for ligand and
> complex. I used -d 1.0 in editconf for the complex simulation and -d 1.6
> for the ligand simulation. Are this values ok? Should I use a different
> value of -d for the ligand simulation?

The value of -d should be set based on the cutoffs used in the simulation 
(inherent to the chosen force field) to avoid minimum image convention 
violations.  Depending on the size of the ligand, you may just want to set the 
box size manually with editconf -box.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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