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

[David]

On Sun, 2003-11-09 at 23:24, Albert Sun wrote:
> 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
> 
> Argon
> 
> [ 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 

chapter 5


>  
> Thanks!
>  
>  
> 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
>         >more?
>         vanderwaals radius is 1
>         >Thanks!
>         > 
> 
> ______________________________________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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