Hello, I have calculated the cumulative number from -cn for the usnic acid solvated by methanol molecules, but this result is enough different to those obtained by integration of the 4*pi*(number density)*area(gr. r2dr) until the first minimum of the RDF. I would like to know how the cumulative number is calculate.
Thanks, Juliana Angeiras Batista da Silva Laboratório de Química Teórica e Computacional Departamento de Química Fundamental Universidade Federal de Pernambuco. ________________________________ De: "chris.ne...@utoronto.ca" <chris.ne...@utoronto.ca> Para: gmx-users@gromacs.org Enviadas: Quarta-feira, 4 de Maio de 2011 14:01:26 Assunto: [gmx-users] free energy Dear Gavin: I'm not seeing a lot of effort on your part to answer these questions. I suspect that you can answer some of this. Good luck! Chris. -- original message -- The current simulations are currently in vacuum. Does the following mdp file seem ok. Note that this is a production run using the final configuration after a lengthy equilibration. Also I was thinking about trying to prevent the other chains from entering the specific site; is there a a way to implement this in gromacs. Gavin chris.neale at utoronto.ca wrote: > yes it will, and so will it affect the profile if water molecules or > ions go in when both chains are absent. > > You'll need to determine what question you are trying to answer and > also think pretty hard about what your PMF really means in the context > of this system. > > Chris. > > -- original message -- > > > Hi Chris > > My windows are restrained obviously using the force constant in the mdp > file. The trajectories that I have viewed are those of the individual > biased sampling windows. I have not put on the unbiased simulations yet. > There is also the following issue: The simulations involve two identical > molecules containing hydrocarbon chains. I calculate the PMF to take a > specific hydrocarbon chain of one molecule out of a specific site on the > neighbouring molecule. When this guest chain goes out, other chains can > go in (intramolecular or intermolecular). Will this affect the profile? > > Gavin -- 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
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