RE: Output only protein .dcd

From: Meric Ayse Ovacik (movacik_at_KU.EDU.TR)
Date: Wed Sep 15 2004 - 02:23:03 CDT

 namd tutorial page 45, you will find the right way to do it. there is the
 tcl script called mk_protein_dcd.tcl that you can find in namd-tutorial
 files...
meric
> ----- Original Message -----
> From: "Nur Aida Abdul Rahim" <aida_at_MIT.EDU>
> To: <namd-l_at_ks.uiuc.edu>
> Sent: Tuesday, September 14, 2004 9:41 PM
> Subject: namd-l: Output only protein .dcd
>
>
> > Hello all,
> >
> > Does anyone know if it is possible to output a .dcd file with only the
> values
> > for the protein in my system? If so, how could I go about doing this?
This
> is
> > because I am only interested at looking at the trajectory of my protein
> > throughout SMD and not the water molecules. My system is ~150,000 atoms
> large
> > and consists of a protein in a waterbox. Running an SMD simulation of
1ns
> long
> > and saving at every 0.5ps produces a .dcd file that is 2GB large. If I
> could
> > output only for the protein, the size of the file would be smaller and I
> could
> > maybe load it onto a .psf of just the protein without surrounding
> water...?
> > Maybe. Any advice would be greatly appreciated, thanks!
> >
> > Aida
> >
>

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