On 7/04/2011 9:23 AM, Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner <mbx0...@yahoo.com <mailto:mbx0...@yahoo.com>> wrote:Elisabeth, You CAN, in fact calculate the contribution of the reciprocal part of the PME energy to the binding energy between two components in a heterogeneous system, its just quite tedious... say, your system is molecules A and B for which you want to know the interaction energy, and the rest of the system, typically the solvent, we call C. Now your total Reciprocal Coulomb energy will have six parts: ER_tot = ER_AA + ER_BB + ER_CC + ER_AB + ER_AC + ER_BC but these parts are NOT given in the gromacs output as they cannot be calculated DIRECTLY, you have to calculate them by setting the charges on A, B, or C (or combinations thereof) to zero (there is a tool for setting the charges in a tpr file to zero) and then do more runs with: "mdrun -rerun" based on the original trajectory to get the required contributions. then E_AB = ER_C0 - ER_A0C0 - ER_B0C0 (or something like it, do double check that formula, i can't be bothered thinking it through now ... here ER_A0C0, for example, is the reciprocal part of the coulomb energy with charges in groups A and C set to zero, etc) this being said ... it's tedious, time-consuming, and error-prone (you need to use double precision and save a lot of frames to get reasonably accurate numbers) You might be better off using reaction field, or PME and simply ignore the reciprocal part altogether (if your molecules A, B are NOT charged and have no permanent and large dipole moment you might get away with the latter) Thanks for your elaborate message.The point is in my case there is no option other than ignoring LR since LR is not covered by shift or switch functions but at least what PME reports for SR is more accurate. So the decomposed Coulmb. SR terms I am getting using energy groups from PME are "reliable ?
The short-range interactions with PME are no longer a 1/r function. See manual section 4.9.1. By design, the modified function decays to zero faster. Whether your observable is perturbed by using any of these modified short-ranged approaches is probably unknown. Conventional wisdom would be that they were all flawed from lack of the long-range contribution.
Mark
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