compute fep and fix wall/reflect

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Dear Lammps Users,

I am using lammps-16Mar18 package with USER-FEP installed.

I am trying to calculate free energy for gas molecule confined in the pore filled with oil solvents.

The pore is finite in X direction with two bulk volumes outside the pore; therefore, during simulations, the gas molecule can move out of the pore.

I would like to ask whether I can use ‘compute fep’ together with ‘fix wall/reflect’ in order to restrict the gas molecule from moving out of the pore for free energy perturbation calculations.

Will ‘fix wall/reflect’ affect the results of free energy from ‘compute fep’?

I look forward to your advices.

Thank you.

Regards,

Anh

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As far as I can understand, the goal of using fix wall/reflect is to introduce a bias in the system and restrict the motion of a given molecule within the pore. If this is the case, then yes it will affect the results because the sampling is not “ergodic” any more. Unless you know how to quantify the contribution of the bias in the free energy of the system, it is better to think of an alternative scheme.

Hope this helps
Regards
Evangelos

Στις Τετ, 24 Ιουλ 2019 στις 12:01 π.μ., ο/η Phan, Anh <anh.phan.13@…2092…> έγραψε: