[gmx-users] what is the force on the energy group when pullcode is used?

1185201182 1185201182 at qq.com
Tue Jul 17 14:55:47 CEST 2018

one more question about the pull code.

I have outputted the force for pulling the molecule in .xvg file. If I pulled the molecule in Z direction, does the positive sign in front of the force mean the direction of the pulling force is identical to the positive direction of the Z axis?


------------------ Original ------------------
From:  "Justin Lemkul";<jalemkul at vt.edu>;
Date:  Jul 17, 2018
To:  "gmx-users"<gmx-users at gromacs.org>; 

Subject:  Re: [gmx-users] what is the force on the energy group when pullcode is used?

On 7/17/18 6:03 AM, 1185201182 wrote:
> Dear users
> I am using the pull code  to pull one of molecules in my simulation and the molecule which is pulled is also defined  as an energy group in my mdp file, then I output the force in trr file
> So I wonder if the force on the pulled molecule in the trr file just includes the force from potentials , or it also includes the force from the pull code.

The forces written to the .trr are not decomposed in any way, so it's 
the total force acting on the atom(s) selected. Energy groups have no 
relevance here.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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