VMD-L Mailing List

From: YangMingjun (mjyang_at_dicp.ac.cn)
Date: Tue Mar 02 2010 - 20:36:25 CST

Dear all,
    I created a system.pdb file corresponding to the system.psf file by VMD. But the atom number beyond 100000 is not displayed normally.
Does it affect the subsequent MD simulation and energy minimization? Or how to fix this problem for normally display?

Part of the system.pdb file is:
-------
...
ATOM 99996 OH2 TIP3 8931 13.511 28.315 -25.647 1.00 0.00 WT7 O
ATOM 99997 H1 TIP3 8931 13.491 29.246 -25.692 1.00 0.00 WT7 H
ATOM 99998 H2 TIP3 8931 13.733 28.131 -26.571 1.00 0.00 WT7 H
ATOM 99999 OH2 TIP3 8932 20.841 35.078 -29.982 1.00 0.00 WT7 O
ATOM ***** H1 TIP3 8932 20.462 35.696 -30.696 1.00 0.00 WT7 H
ATOM ***** H2 TIP3 8932 21.427 35.666 -29.452 1.00 0.00 WT7 H
ATOM ***** OH2 TIP3 8935 8.519 28.077 -34.237 1.00 0.00 WT7 O
ATOM ***** H1 TIP3 8935 9.441 28.048 -34.615 1.00 0.00 WT7 H
ATOM ***** H2 TIP3 8935 8.109 28.653 -34.850 1.00 0.00 WT7 H
ATOM ***** OH2 TIP3 8936 15.538 37.379 0.451 1.00 0.00 WT7 O
ATOM ***** H1 TIP3 8936 14.638 37.245 0.108 1.00 0.00 WT7 H
...
-------

Many thanks.
 
 Yang Mingjun

2010-03-03

-----------------------------------------------