Re: namd force field

Date: Tue Nov 22 2011 - 12:14:28 CST

Some people have already tried a simular thing to implement a hybrid Coarse Grained/Al lAtom potential (for Martini).

Take a look at here Phys. Chem. Chem. Phys., 2011, 13, 10437–10448. Maybe you can take something useful from that.





----Mensaje original----De: akohlmey_at_gmail.comFecha: 22-nov-2011 11:05Para: "Molecular Dynamics"<>CC: ""<>Asunto: Re: namd-l: namd force fieldOn Tue, Nov 22, 2011 at 7:21 AM, Molecular Dynamics<> wrote:> Dear Namd users,>> I want to run md simulations for binary mixtures consisting of X and Y type> molecules. I have some questions about generating topology and parameter> files. Is it possible to model the molecule X in the mixture with united> atom representation that treats &ndash;CHx groups as single interacting site and> the molecule Y with all atom representation that treats each atom as a> site in CHARMM19 force field?possible: yes. meaningful: perhaps, but you have to find that out for yourself.all that a classical MD code sees are a bunch of coordinates with associatedmasses, charges and potentials. it doesn't care at all what it represents allthe MD code does is evaluate the potentials. the rest is up to the user andfollows the simple rule: garbage in, garbage out.cheers, axel.>> Thanks for your help.>>-- Dr. Axel of Science and TechnologyTemple University, Philadelphia PA, USA.

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