2009/7/20 Vitaly V. Chaban <[email protected]> > Hi Matteus, > > Yeah, dynamic groups would be a powerfull tool. But such mechanism is still > under development if I am not out-of-time. > > The possible way to proceed with such kind of research (as Berk advised me > here long ago) is to sort the trajectory (trjorder) based on the distance > criteria. Then you can make an index file with N first numbers (which are > close to the protein) and use g_energy with this group and protein group. It > seems for your task this way is a perfect solution. >
Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use g_energy? This way you would be free of any problems with molecules going in and out of your solvation shell, if I am getting things right.
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