VMD-L Mailing List

From: Dongsheng Zhang (dong_at_pampas.chem.purdue.edu)
Date: Wed May 21 2003 - 23:13:52 CDT

To Whom It May Concern,

I am a new user of VMD. I have two questions. One is for displaying.
Another one is for making a movie.

1. I got some trajectory files in YASP format (it is a binary file, I
can't show you the format) for model polymer crystallization. Because
there is no real atom in polymer, it seems hard to display it. I have
done it successfully for short chains by the following process: first
transfer YASP file to PDB file by using poly2pdb. The format is

REMARK 4 Generated by poly2pdb
REMARK 4 Description:
HETATM 1 C UNX 1 15.707 -11.100 9.006
TER 2 UNX 1
HETATM 3 C UNX 1 15.691 -10.659 9.254
TER 4 UNX 1
HETATM 5 C UNX 1 15.662 -10.191 9.417
TER 6 UNX 1
HETATM 7 C UNX 1 15.585 -9.739 9.612
TER 8 UNX 1
.
.
.
CONECT 1 3
CONECT 3 1 5
CONECT 5 3 7
CONECT 7 5 9
.
.
.
MASTER 2 0 0 0 0 0 0 0 19200 19200 19200 0
END

If I display this directly, the error message is
MolAtom 14457: Exceeded maximum number of bonds (8).

Therefore I transfer this PDB file to XYZ file, modify the distance
between two monomers, change the atom type to Oxygen, and transfer XYZ
file to PBD file by babel. For a system with short chains (20 monomers),
it works fine. I can make a movie by making a dcd file. However, for
long chains (100 monomers), it doesn't work, but it surprised me that it
seems be able to display 10 chains, but not the whole system (192
chains). Could you please tell me how to use VMD for model polymer?

2. How to adjust the speed for movie? If I use vmdmovie from tools manu
and save it as mpg file. It shows too fast. Could you please tell me how
to adjust it? Can I modify the movie script? If I can, please give me
some hints.

Thank you very much for your help!

Dongsheng Zhang