Hey Denis Thank you very much for clarifications.
-- sikandar On Mon, Oct 11, 2010 at 1:23 PM, Denis Andrienko <[email protected]>wrote: > 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] <votca%[email protected]>. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- 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.
