Dear Dr. Anselm Horn,
Regarding the function LIE (linear interaction energy) from cpptraj for calculating the interaction energies between two masks, the results generated from this analysis refer to either an energy difference (DEAB = EAB - EA - EB ) or the absolute energies (EAB) ?
Sincerely,
Eduardo.
________________________________
De: Eduardo R. Almeida <eduardoe.r.a.hotmail.com>
Enviado: terça-feira, 9 de março de 2021 17:04
Para: AMBER Mailing List <amber.ambermd.org>
Assunto: Re: [AMBER] Pair interaction energy
Dear Dr. Anselm Horn,
Thank you for you response! I will test this function (lie) with my system.
Best regards,
Eduardo.
________________________________
De: Dr. Anselm Horn <anselm.horn.fau.de>
Enviado: terça-feira, 9 de março de 2021 16:50
Para: amber.ambermd.org <amber.ambermd.org>
Assunto: Re: [AMBER] Pair interaction energy
Dear Eduardo,
maybe the linear interaction energy feature from cpptraj is what you are
looking for. The name of the command is lie, and you can specify two
masks, between which the interaction energy (vdw, ele) is computed for
each frame of the trajectory specified.
Regards,
Anselm
On 03/09/2021 03:53 PM, Eduardo R. Almeida wrote:
> Dear Amber users,
>
> I would like to know if there is a function in cpptraj to calculate the pair interaction (van der Waals + electrostatic) between two entities over a trajectory. In the manual (Amber 18), I saw the pairwise function, but I do not know if this function calculate the pair interaction energy, since I did not see how to specify two masks for this calculation. Maybe, there is another method/function for analyzing these energies, without manually calculated them (DEAB = EAB - EA - EB) from the potential energies generated from the molecular dynamics simulation. Could anyone help me with this question?
>
> Sincerely,
>
> Eduardo.
>
>
>
>
>
>
>
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Received on Tue Mar 09 2021 - 15:00:02 PST
