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Re: [lammps-users] FEP calculation on charged cluster

# Re: [lammps-users] FEP calculation on charged cluster

 From: Imanuel Kristanto Date: Thu, 23 Nov 2017 19:43:25 +0900

Dear Dr. Paquay and Prof. Padua,

Many thanks for your suggestions, comments, and of course your time to explain in depth how to solve my problem.
These definitely will help me to understand better about free energy methods and how to apply it correctly.
I will study more and retry to calculate the system as per your suggestions.

On Thu, Nov 23, 2017 at 7:18 PM, Agilio Padua wrote:
I think your questions are more about free energy methods than about LAMMPS. I can think of two different issues:

Your system not being charge neutral. See P. H. Hünenberger and J. A. McCammon, J. Chem. Phys., 1999, 110, 1856. I had more references but can’t find them now.

Something with the setup. You can try to calculate just the energy difference between the initial and final states by changing the parameters in the input file and see if the results make sense.

Agilio

On 23 Nov 2017, at 02:01, Imanuel Kristanto <imanuelkristanto@...24...> wrote:

I have one question in regards to your comment, you said that if it is increased (by +0.1) it will increase the repulsion hence higher chemical potential. How about, if I reduce the charge by varying initial charge (lambda * (+1 charge)), with lambda 1.0 to 0.1? In my understanding, since initial charge of each silver atoms is about +1, if lambda equals to e.g. 0.5, the total charge of  the cluster should be lower, thus I expect lower free energy compared to lambda = 1.0. Please correct me if I am wrong in implementing FEP calculation.
Thank you.

On Wed, Nov 22, 2017 at 11:08 PM, Agilio Padua wrote:
If the atoms in the cluster have charges of the same sign and they are increased in your perturbation (by +0.1) I would expect the chemical potential to go up due to repulsion.
Maybe I’m missing something.

Agilio

On 22 Nov 2017, at 02:21, Imanuel Kristanto <imanuelkristanto@...24...> wrote:

Some clarification on the system details.
The charge is not neutral during FEP calculation (the original charge is +1 after equilibrated by QEQ, the charge of each silver atom varies from 0.84-1.15). Additionally, for interaction between silver atoms are described by EAM potential.
So the unperturbed charge is based on QEQ equilibration is around 0.84 to 1.15.

On Wed, Nov 22, 2017 at 1:27 AM, Agilio Padua wrote:

Is your system kept charge neutral during the FEP calculation? There can be large long range effects if not.

I don’t understand what is the unperturbed state: charges +1 or QEQ charges? If the latter, what are the typical values?

Agilio

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Best Regards,
Kristanto

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Best Regards,
Kristanto

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Best Regards,
Kristanto