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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: Stefan Paquay <stefanpaquay@...24...>
Date: Wed, 22 Nov 2017 21:08:43 -0500

I remember getting signs right is always a pain with free energy calculations. Double check exactly what you're calculating and what compute fep calculates, maybe there's a minus missing somewhere or you are calculating F_(uncharged) - F_(charged), which would be negative if the charges are purely repulsive. 

On Nov 22, 2017 8:02 PM, "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@...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@...92......> 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






--
Best Regards,
Kristanto




--
Best Regards,
Kristanto

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