VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 29 2008 - 15:06:49 CST

When you say "initially everything is fine", that would indicate to me
that you are expecting VMD to recalculate the bonds on-the-fly, which it
can do, but not by default. By default, VMD will keep the same bond pattern
over an entire simulation trajectory unless you use the DynamicBonds
representation, or similarly set flags that force dynamic bond recalculation
for the other ball-stick type representations. If the bond looks "long"
as the simulation progresses, it is because your atoms are moving apart
but the bond connectivity has not been recalculated. I'd be more concerned
about your simulation than the display of the bond in VMD, since this is
all coming from your trajectory data.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 29, 2008 at 11:01:10PM +0200, OZGE ENGIN wrote:
> I use Gromos 53A6 force-field and initially everything is fine.
>
> -----Original Message-----
> From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
> To: OZGE ENGIN <OZENGIN_at_KU.EDU.TR>
> Date: Fri, 29 Feb 2008 14:47:55 -0500 (EST)
> Subject: Re: vmd-l: unusual bond between the cysteine and arginine residue during the simulation
>
> On Fri, 29 Feb 2008, OZGE ENGIN wrote:
>
> OE> Hi all,
> OE>
>
> OE> I perform a simulation of a 24-residue peptide at air/water
> OE> interface. While I am looking at the trajectory, I see that there is
> OE> an unusual bond (long bond) between the cysteine and arginine
> OE> residue. However, I have another cysteine residue but it does not
> OE> make any bond with any other residue.Both residues are charged.
>
> OE> What may be the reason?
>
> bonds are taken from the .psf file (i assume you use NAMD
> and load .psf and .dcd), so your .psf file is not correct.
>
> axel.
>
> OE> Ozge Engin
> OE> =================================
> OE> Computational Science & Engineering
> OE> Koc University
> OE>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University 

-- 
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