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


From: Agilio Padua <agilio.padua@...24...>
Date: Thu, 23 Nov 2017 11:18:38 +0100

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:

Dear Prof. Padua,

Thank you for reply and comments.
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 <agilio.padua@...12...24...> 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:

Thank you for your reply and thoughtful comments.
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 <agilio.padua@...24...> wrote:

I was trying to understand your problem but have some questions about your setup:

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