Hey Denis The similar method ( as you described) is mentioned in GROMACS tutorial pages under the Pull-Code technique. I am a bit confused here about Many-Body PMF and Two-Body PMF. When you constrain two particles ( in solvent environment) and compute forces, that force also contain contribution from solute-solvent interactions along with solute-solute. So how is that two-body PMF? I understand that in limit of zero density i.e. to say just two particles/atoms/molecules , PMF has only two body interaction effects. But with finite density you have multi-body effects.
Alternate approach which I am trying to compute PMF for water using MD bulk trajectory is that, I select one water molecule Oxygen as reference point, then step radially outward by binning. Compute the avg force on water molecule in bin located at r, take the component of that force in radial direction (i.e. f.r) . Using this force information I integrate from last bin to first to compute PMF. But this PMF does not satisfy Boltzman relation with g(r). So I am having doubts about this method and my understanding of two-body /multi body PMF. I really appreciate your patient and quite explanatory responses to my question. I have just began my work in this field, and trying to get hold of different aspects of it. thanks sikandar On Fri, Oct 8, 2010 at 1:40 AM, Denis Andrienko <[email protected]>wrote: > Hi Sikandar, > > One can constrain two particles at a specific distance (r) and then > run MD with this constraint. The force on the constraint will give you > PMF(r). This is normally used when you have a very dilute system (e.g. > solute/solvent system and solute-solute PMF). In this case it is > difficult (impossible?) to obtain g(r) with a reasonable accuracy. > > We have the scripts but you will have to adapt them to your > environment. Send an email to Sasha Lukyanov (lukya...@mpip- > mainz.mpg.de) if you want to have them. > > Best, > 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.
