[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

Peter C. Lai pcl at uab.edu
Mon Apr 11 08:02:17 CEST 2011

Any rationale behind the thermostat coupling of a ligand with the protein
instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme
binding example)? Especially with small drug-type molecules as generally the 
ligand might/would take the usual place of solvent within a binding region 
or other solvent accessible surface and it might be more realistic to 
simulate the ligand as part of the solvent's ensemble (one might run two
simulations in order to compare the ligand-protein interaction to the 
water-protein interaction at the interaction interface...)

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
(205) 690-0808               |

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