VMD-L Mailing List

From: Ana Celia Araujo Vila Verde (avilaverde_at_engr.psu.edu)
Date: Tue May 23 2006 - 11:36:54 CDT

Hi,

 

I made a pdb and a psf file for gold, to be used in NAMD. I have three questions:

 

1 - when I make the bond list in VMD, is it a problem if I repeat bonds? For example, let's say that atom 1 is connected to atom 2. In the bond list, should I list this bond just once ( "1 2") or can I list it twice ("1 2 2 1")? Also, if I only list it once, does it matter if I use "1 2" or "2 1"? I couldn't find information about this.

 

2 - I will use periodic boundary conditions in my simulation. So, my crystal should also be periodic. Should I just list the realistic bonds or should I also include the bonds that make the crystal periodic? Here's a 1-dimensional example:

The realistic bonds are 1-2, 2-3, 3-4. However, to make this 1-dimensional crystal periodic, I need to connect 1 to 4. So, should the psf include bond "1-4"?

 

1-------2-------3---------4

 

3- I currently have a pdb and a psf already done. My current psf includes repeated bonds (like I described above in 1) and also includes the bonds that make the crystal periodic. When I load both the pdb and the psf file into vmd, vmd is unable to display some of the bonds correctly: some bonds do not appear at all, even though they are listed in the psf file. Also, VMD also shows the bonds between atoms in the extremities of the crystal (corresponding to the 1-4 bond described above in 2).

 

I'd really appreciate some insight into this, since I couldn't find a detailed description of the psf files that answered my questions.

Best regards,

 

Ana

 

_________________________________

Ana Célia Araújo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802

USA

 

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

avilaverde_at_engr.psu.edu

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