VMD-L Mailing List

From: YangMingjun (mjyang_at_dicp.ac.cn)
Date: Wed Mar 03 2010 - 00:52:07 CST

Dear Dipesh,
  Then how should I do when my system is larger than 100000 atoms?

        Many thanks.
Mingjun
2010-03-03
--------
State Key Lab of Molecular Reaction Dynamics (SKLMRD),
Dalian Institute of Chemical Physics (DICP),
Chinese Academy of Sciences (CAS).
Zhongshan Road457, Dalian City, 116023, China.

------------ At 2010-03-03 11:42:16 you wrote: -------------
From: Dipesh Bhattarai
Sent: 2010-03-03 11:42:16
To: YangMingjun
CC: vmd-l
Subject: Re: vmd-l: display of the atom number beyond 100000 in pdb file

I think this is due to the pdb file format. It only allows for 5 digit
number. So basically you cannot have more than 99999 atoms.

Dipesh

On Tue, Mar 2, 2010 at 8:36 PM, YangMingjun <mjyang_at_dicp.ac.cn> wrote:

> 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
>
> -----------------------------------------------
>
>
>
> 

-- 
Dipesh Bhattarai, PhD
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