[gmx-users] RE: evb and mapping potentials

[rsf]

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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-- 
****************************************
Romelia Salomon
Miller Group
132 Noyes
Chemistry Department
Caltech