[gmx-users] PME

Mark Abraham 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:
>     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 

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