Hi, I think that you could use the free energy parts of gromacs for your purposes.
V1 and V2 can be coupled via a parameter lambda, such that (assuming you're not changing masses/atoms) H(p,r,lambda) = (1-lambda)* V(A-B + C) + lambda*V(A + B-C). IN the manual it is described how to inform gromacs what V(A-B + C) and V(A + B-C) are. For new bonds, angles etc, define them all, but let the forceconstants and equilibrium constants be 0 in one state, like: A-B 1 r_e k 0 0 B-C 1 0 0 r_e k For driving it, you can perform the MD at discrete lambda values along the 0,1 interval. Hope this helps. Best, Gerrit > Hi > > Thanks for you answer, what I want to do is to study a reaction with MD > > A-B +C -> A+B-C > > , for that I am representing it by a two state system in an EVB > representation, where I have my transferring group, B, attached to A in > the first state(V1) and to C in the second(V2). I am describing the > off-diagonal elements as a constant parameter fitted form experimental > data to reproduce the experimental free energy profile. > > To sample the space I would like to drive the reaction using a mapping > potential of the form > > Vmap= V1 + lamda*(V2-V1), with lambda ranging from [0.0,1.0]. > > Therefore I would have to get gromacs to run on the potential surface > generated by the mapping potential, which is a mixture of my two diagonal > states. I have been trying to see if gromacs can deal with this situation > with the present implementation, but I can't seem to find what I need. I > can also program it in myself, but I would like to know if someone has an > idea of how to do it properly within the existing framework of gromacs, or > if someone is aware of some way of getting the current version of gromacs > to do what I need. > > The difference between both states would be some topology parameters > (charges, bonds, angles, dihedrals) as well as connectivities that > describe the chemically active part of the system. > > Thanks so much for your comments. > > Romelia > >>> 6. EVB and mapping potentials (rsf) >>> >>> >> Hi, >> >> I do not understand your question, but what you try to do seems >> interesting. >> >> This is how far I got: >> >> If you have only two states to interconnect, the diagonal elements would >> be the energy H(lamda=0) and H(lamda=1). The off diagonals then have to be >> parametrized as a function of lambda? Would diagonalization then give you >> the forces on lambda? >> >> We have a version of gromacs which supports lambda dynamics, but I am not >> sure if that's what you need? >> >> Best, >> >> Gerrit >> >> >> >>> Hi >>> >>> I want to describe a reaction for what I have a system described by two >>> different connectivities and need to run an MD calculation on a mapping >>> potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal >>> elements of the evb matrix and C is a parameter. Does gromacs have >>> support >>> for running something like this?. Which would be the best way to run >>> this >>> calculation with the standard code, or should I modify it in order to do >>> that. The states have some atoms with different connectivity between >>> them, >>> different forcefield parameters and different charges, the atom types >>> are >>> the same for both. >>> >>> >>> Thanks for your comments. >>> >>> >>> Romelia. >>> >>> -- >>> **************************************** >>> Romelia Salomon >>> Miller Group >>> 132 Noyes >>> Chemistry Department >>> Caltech >>> >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> 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/search before >>> posting! >>> >>> End of gmx-users Digest, Vol 65, Issue 81 >>> ***************************************** >>> >>> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> >> > > > _______________________________________________ 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/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/mailing_lists/users.php
