Mark.Abraham at anu.edu.au
Thu Apr 7 02:56:25 CEST 2011
On 7/04/2011 9:23 AM, Elisabeth wrote:
> On 6 April 2011 15:01, Michael Brunsteiner <mbx0009 at yahoo.com
> <mailto:mbx0009 at yahoo.com>> wrote:
> 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
> thinking it through now ... here ER_A0C0, for example, is the
> 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
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