VMD-L Mailing List
From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 09 2015 - 17:46:00 CDT
- Next message: Marawan Hussien: "Immediate Postdoctoral Position Opening"
- Previous message: Gianluca Interlandi: "Re: measure sasa not consistent"
- In reply to: Gianluca Interlandi: "measure energy"
- Next in thread: John Stone: "Re: measure energy"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
I found the answer myself. It calculates the energy only between two
atoms. For example:
measure energy bond {1 2} k 1 x0 1
The values used are just dummies.
Gianluca
On Thu, 9 Apr 2015, Gianluca Interlandi wrote:
> Dear list,
>
> Starting with version 1.9.1 the measure command of VMD can also calculate the
> energy:
>
> energy energy_term atom_list [parameters] [options]: Returns the specified
> energy term for a given set of atoms. The energy term must be one of bond,
> angle, dihed, imprp, vdw or elect where vdw stands for 'van der Waals' and
> elect for electrostatic energy. The energy is computed based on the CHARMM
> force field functions, the given parameters and the current coordinates.
>
> However, I cannot find an example how to use it. Is "atom_list" just two
> atoms or can it be multiple atoms? Based on the parameters, it looks like it
> calculates the energy between two atoms.
>
> Thanks,
>
> Gianluca
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
- Next message: Marawan Hussien: "Immediate Postdoctoral Position Opening"
- Previous message: Gianluca Interlandi: "Re: measure sasa not consistent"
- In reply to: Gianluca Interlandi: "measure energy"
- Next in thread: John Stone: "Re: measure energy"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]