[gmx-users] Simple L-J Particles' simulation

Albert Sun albert_sun9 at yahoo.com
Sun Nov 9 23:26:01 CET 2003

Hi, David
Thank you very much!
I got a .top file for Simple L-J simulation from you a few weeks ago.
I  added in another type of atom C into this .top file, as below 

[ defaults ]

; nb-function combinationrule

1     2

[ atomtypes ]

; type mass charge ptype sig eps

AR  15.011    0.0   A    0.12340E-02    0.23574E-05 

C    12.011    0.0   A    0.23402E-02    0.33740E-05 

[ moleculetype ]

; molname nrexcl

Argon 1

Carbon 2

[ atoms ]

; id at type res nr residu name at name cg nr

1  AR  1  Argon  AR  1 

2  C    2  Carbon  C   2

[ system ]

; systemname


[ molecules ]

; molecule number

Argon 1000

Carbon 729

But  when  grompp, it had errror messgae   

Fatal error: Moleculetype Argon contains no atoms

Do you know any problem in the modified .top file 

David van der Spoel <spoel at xray.bmc.uu.se> wrote:
On Sat, 8 Nov 2003, Albert Sun wrote:

>Hi, David, 
>I could not understand why I can ONLY have 1 particle per cubic length unit, not
vanderwaals radius is 1

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