VMD-L Mailing List

From: Jerry Xu (jerryx_at_hotmail.com)
Date: Thu Jul 15 2004 - 17:00:27 CDT

okay, thanks.... seems I have to build psf file "by hand". CHARMM is a great
software but really provide a terrible procudure to build a successful psf
file. Hope they can finally make a better one in short future.

Thanks.

>From: Bogdan Costescu <bogdan.costescu_at_IWR.Uni-Heidelberg.De>
>To: Jerry Xu <jerryx_at_hotmail.com>
>CC: vmd-l_at_ks.uiuc.edu, <yxu3_at_lsu.edu>
>Subject: Re: vmd-l: vmd psfgen problem with CHARMM
>Date: Thu, 15 Jul 2004 23:21:22 +0200 (CEST)
>
>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
>

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