[gmx-users] Re: gmx-users Digest, Vol 65, Issue 83 6. EVB and mapping potentials (rsf)

[Gerrit Groenhof]

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
>>>
>>>
>>>
>>>
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>>>
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>>> End of gmx-users Digest, Vol 65, Issue 81
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>
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