VMD-L Mailing List
From: Bogdan Costescu (bogdan.costescu_at_IWR.Uni-Heidelberg.De)
Date: Thu Jul 15 2004 - 16:21:22 CDT
- Next message: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Previous message: Andrew Dalke: "Re: Elliptic molecules"
- In reply to: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Next in thread: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Thu, 15 Jul 2004, Jerry Xu wrote:
> I am just wondering how I can put these atoms into several groups
I'm sorry but I can't help you here...
Only one suggestion: you can look into the topology files that come
with CHARMM (toppar directory) and see how the groups are defined
there. For a small system, you might be able to construct the groups
"by hand".
> re-compile charmm with large or xxlarge limitation...
This won't work. The parameter that I mentioned earlier is not
modified depending on the system size. One thing that you can try is
to modify the value of this parameter, but:
- I don't know if this will break something else (some presumption
that this parameter is smaller than another one...)
- you'll have to increase it to accomodate your whole molecule, which
might mean making it an order of magnitude larger !
- I don't know how CHARMM will work in general with such a big group.
I guess that electrostatic interactions will be off completely... so
CHARMM won't be able to do anything useful.
-- Bogdan Costescu IWR - Interdisziplinaeres Zentrum fuer Wissenschaftliches Rechnen Universitaet Heidelberg, INF 368, D-69120 Heidelberg, GERMANY Telephone: +49 6221 54 8869, Telefax: +49 6221 54 8868 E-mail: Bogdan.Costescu_at_IWR.Uni-Heidelberg.De
- Next message: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Previous message: Andrew Dalke: "Re: Elliptic molecules"
- In reply to: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Next in thread: Jerry Xu: "Re: vmd psfgen problem with CHARMM"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]