[gmx-users] Sampling a weak ligand

[Александр Лашков]

Also, you may use the pull code in gromacs,
Alexander

вт, 24 дек. 2019 г. в 07:47, Александр Лашков <alashkov83 at gmail.com>:

> May be you should add intermolecular interaction as is in FEP calculation
> for protein-ligand complex.
> Alexander Lashkov
>
> вт, 24 дек. 2019 г., 3:05 Raphaël Robidas <raphaelrobidas at gmail.com>:
>
>> Hello all,
>>
>> I am running free energy perturbation calculations to determine the
>> absolute affinity of a weak ligand. To prevent dissociation and increase
>> sampling, the first few lambda states introduce a harmonic restraint via
>> the intermolecular interactions feature. The problem is that my ligand
>> dissociates in the first state, which has no restraint at all. Is there a
>> technique to still get an accurate value? I plan on running a longer
>> simulation for the first state in order to sample more the bound state,
>> but
>> I hope that there is a smarter way!
>>
>> Thanks and happy holidays!
>> --
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>