From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Dec 14 2016 - 13:53:02 CST
On Wed, Dec 14, 2016 at 2:47 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
>
> Second question. When I use the NAMD Energy plugin in VMD on a dcd file,
>> the electrostatic energy is a bit different from that reported in the namd
>> log file (about 10% different).
>
>
> How about the kinetic energy? Velocities are absent in a DCD trajectory
> file.
>
Apologies, I hadn't noticed that you referred to electrostatic energy.
Keep in mind that cutoffs and PME grid spacings that the plugin sets may be
different from the ones you set in your own NAMD input.
>
>
>> What could be the cause of this? Also, what goes into the conformational
>> energy reported by this plugin? It doesn’t seem to be a sum of other
>> energies, that I can tell …
>>
>
> See the brief documentation to the NAMD energy plugin:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
> If you had read that thoroughly, you would seen the expression
> "conformational energy (bonds, angles, dihedrals, and impropers)". Does it
> not correspond to the sum of those terms?
>
> Giacomo
>
>
>
>
>>
>> Thanks.
>>
>> Chris
>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213 <%28215%29%20204-4213>
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we
> run the computers instead of the computers running us."* - Steve Oualline
>
>
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 <(215)%20204-4213> Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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