Just to clarify...
The statement that "alignAxes" may fail in case of membrane systems (lipid only of lipid+protein) is because these systems are very sensitive to the alignment of the X, Y and Z coordinates due to PBC condition. Then even small particularities in the moment of inertia of the system may change the proper orientation upon the geometrical transformation (translation and rotation), leading to beak the membrane's continuity and generating issues during the MD...
That is way a having a "translate to COM" command is so important...
Best,
Matías
----- Mensaje original -----
De: "Matias Machado" <mmachado.pasteur.edu.uy>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 24 de Diciembre 2020 18:57:13
Asunto: Re: [AMBER] Position of the solute (center of mass) in the simulation box
Dear Eduardo,
It can be done, but it requires two interactive steps...
First you must execute the command "center unit" to print on screen the center of mass of the unit, let say {x y z}.
Then you have to manually translate the unit by executing "translate unit {-x -y -z}".
Note: replace "unit" by the actual name that you are using for the unit...
Alternative, you can try the command "alignAxes unit", which may do the same in one step, but it may fail in case of membrane proteins, at least in my experience...
By the way, neither "center" nor "alignAxes" are present in the AMBER 20 Manual, however you can typing "help" at LEAP command line to see the list of available commands and "help command_name" to access the specific help.
[Note for developers]
It would be very handy to have a command (or option in "translate") to do it at once.
Additionally, allowing to get the value from the command "center" and to do some math with it would also be nice.
Best regards,
Matías Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Eduardo R. Almeida" <eduardoe.r.a.hotmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Jueves, 24 de Diciembre 2020 10:07:04
Asunto: [AMBER] Position of the solute (center of mass) in the simulation box
Dear Amber users,
I would like to know if it is possible to define a position for the center of mass (COM) of the solute in a simulation box by using the xleap/tleap programs. I'm asking it since I saw that in the Gromacs package one can define a position for the COM of a solute, for example at (3.280, 2.181, 2.4775)nm in a box dimensions (6.560, 4.362, 12.000) nm. If so, could someone help me ?
Sincerely,
Eduardo.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 24 2020 - 14:30:02 PST
