From: Tushar Jain <jain.tush@gm...>  20050224 22:00:02

Hi, I am currently working in the McCammon group. I am interested in using APBS with advanced MonteCarlo(MC) sampling strategies. I have managed to link and run APBS from within the C code that performs the MC moves. Since only a few atoms change positions from one snapshot to the next, I was wondering if there was a way to speed up APBS for the calculating the energies of the new configuration, namely perform "incremental calculations", since the electrostatic field will be largely the same at distances far away from the moved atoms. More specifically, I had the following questions: 1) Is there a way to pass APBS the solution from the previous iteration? Would such a strategy be useful in reducing time for the new solution? 2) In the case of focussing calculations, a call to initMG destroys the pbe and pmg objects of the previous calculation. Is this necessary if the goal is to reuse or repopulate these objects for incremental solutions? 3) Have any of the users implemented such incremental calculations or have insights about the best course of action to accomplish the above? Thanks, Tushar. 