> > Message: 1 > Date: Wed, 07 Sep 2011 12:01:00 +0200 > From: "Emanuel Peter" <emanuel.pe...@chemie.uni-regensburg.de> > Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations > To: <gmx-users@gromacs.org> > Message-ID: <4e675cfc020000f100014...@gwsmtp1.uni-regensburg.de> > Content-Type: text/plain; charset="iso-8859-1" > > At first I would like to say that I deeply apologize for > the cave-like things I have said. I again say, that this > was not the field I am deeply involved. >> From Gerrit I got a banana. > For this guy, I am a cave-man.
No, a monkey, just like you signed one of your earlier mails. The questions you raise are all unaswered, but extremely relevant. Futher open discussion is highly appreciated. > > Generalized forces and averages for H+ interchange ? The idea is that the protons are degrees of freedom. Protons can thus appear "spontaneously" on titrating sites. The driving force is the thermodynamic force: DG/Dl. More details can be foudn in the papers By Charly Brooks, JAna Khandogin and ourselves. > Comparison with titration experiments ? Not many of these around, but these will be crucial to establish the validty of the different approaches. > Is there any experimental evidence for the rates of > interchange ? NMR maybe. > Are simulation-times or the periods of interchange at > any time realistic? Probably not. > Are equilibria sampled well, with such interchanges, > or are there jumps in free energy by this interchange ? No the system follows the underlying free energy landscape always. THerefore there are no jumps, as one may habe in MC approaches. However, the price one pays is that one does sample intermediate state, in which the proton is only partially there. > Why is there no free H+ ? That would give an enormous sampling problem. Furthermore, the properties of MM hydroniom are very different from real hydronium Hope this adds to the discussion. Gerrit -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
