From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Apr 09 2015 - 23:51:42 CDT

Thanks John,

I am using VMD to perform Monte Carlo simulations and I need to evaluate
the CHARMM force field energy. So far, I have been writing the PDB after
the move to disk and then called gromacs to evaluate the energy. However,
I found that I need better control over the single energy terms. I am
considering NAMDenergy, but even with that I would still have to write a
PDB to disk and then read it into NAMDenergy, right? Or, is there a way
through iMD to update the coordinates held by NAMD so that the energy
evaluation can be done more efficiently?

Thanks,

      Gianluca

On Thu, 9 Apr 2015, John Stone wrote:

> Hi,
> The number of atoms depends on the energy term being measured
> (bonds, angles, dihedrals, etc). This was a special feature added
> to VMD in support of the older "paratool" force field parameterization
> plugin. If you're interested in doing more sophisticated energy evaluations
> you may prefer to use namdenergy at present. There may be another way of
> computing energies in a future version of VMD depending on how developments
> progress...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Apr 09, 2015 at 03:39:49PM -0700, 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.
>> -----------------------------------------------------
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>

-----------------------------------------------------
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.
-----------------------------------------------------