From: Samoylova, Olga M. (Olga_Samoylova_at_baylor.edu)
Date: Tue Apr 15 2014 - 12:50:06 CDT
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Kenno Vanommeslaeghe [kvanomme_at_rx.umaryland.edu]
Sent: 15 April 2014 12:13
To: NAMD list
Subject: Re: namd-l: Nanotube Simulation
On 04/15/2014 10:49 AM, Samoylova, Olga M. wrote:
> PS. I have a question to more experienced audience. Am I right if I put 0
> for impropers? I just compared the .psf files created by the script
> make_arm.tcl (no impropers) and psf file from vmd nanotube builder (which
> has improper parameters even if i didn't choose impropers in topology
> building options). If I try to run simulations with impropers I have error
> about these parameters. If I put 0 - everything works. I would appreciate
> any advice about it.
It depends on whether the force field requires impropers there or not.
CHARMM doesn't; if it would be me using CHARMM FF, I would remove the
impropers on the carbon nanotube from the psf file altogether, or even
better, tell the tool that created the psf file that you don't want them
to be generated in the first place. The energy is the same in all 3 cases
(setting to 0, removing, preventing generation); I just feel preventing
generation is the cleanest and safest way to do it. Again do note that
other force fields might require nonzero impropers!
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