W dniu czwartek, 11 lipca 2013 12:50:13 UTC+1 użytkownik Tristan Bereau napisał: > > Hi Steven, > > Any equilibrium thermodynamic quantity, such as a RDF, cannot depend > on the masses of the system (they only couple to the particle > velocities, not to the interaction potentials). So your calculation > cannot depend on the beads' masses. Look out for masses only if you're > interested in dynamics. > > Best, > Tristan >
Hi Tristan, Thanks. I am not sure about your statement. If you change mass the velocities are changed so the positions are changing... if the position is changed then the RDF is changed as its with respect to the distance between group of atoms. Thinking experimentally, we did some ITC measurements - free energy and in the molecular weight of the protein had influence on the free energy. Many models e.g. small molecules binding given protein depends on two factors: molecular weight and logP value of the small molecule. Do you know whether Iterative Boltzmann inversion producing tables for intermolecular potential uses always combination rule 1: com-rule in gromacs [defaults]? Steven > > On Thu, Jul 11, 2013 at 1:45 PM, <[email protected] <javascript:>> > wrote: > > Dear Users, > > > > My polypeptide has 90 residues. I divided them into 5 type of beads. For > > example lets take the example of basic residues (type B) - I have > Lysine, > > Arginine and Histidine and acidic (A) only one Aspartic Acid and one > > Glutmaic acid so two in total. I wish to assign different mass to each > of > > them but they belong to the one type. > > > > How I can I specify this in gromacs topology so Votca will calculate RDF > > after each step between e.g. A and B? > > > > > > Another issue: potential between Acidic - Acidic. As i have two Acidic > > residues only I specify RDF between A1 and A2. But then Votca will > calculate > > RDF between A-A so twoA-twoA which I do not wan to. If specify them > > separately so two types A1 and A2 instead of type A Votca will calculate > > wrongly A1-B and A2 - B and I wish to have A-B. > > > > Would you advise? > > > > Steven > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to [email protected] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
