Hi Sikandar, The procedure you are describing will not give you PMF. I don't even know what exactly this is going to be.
An alternative approach would be to fix the positions of the centers of mass of two water molecules at a distance r and measure a total force (r) on each of them during the MD run. Integrating this force as a function of r you will obtain PMF. This of course requires a special MD run and is similar to the pull code, except you don't have to subtract the rotational entropy at the end. cheers, Denis -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
