[gmx-users] gettin a amorhous system??

[Mark Abraham]

pushyami atluri wrote:
> hey,
>  i am trying to simulate zirconia and i have mentioned my efforts before.
> when i am trying to simulate a simple 4nm particle at the end of the run 
> i get a amorphous system.same thing when i am trying for a 10nm particle 
> the run takes a pretttttyyyyyyy long  time to even start.the 4nm 
> particle run finishes in 20 min and for the 10nm it doesnt even start in 
> 40 minutes.so can u pleasee tell me what can be the problem..is it just 
> the processor speed or t values of forces going bersek because i get a 
> amorphous system at the end???

Would you want to read this and spend your valuable time trying to help 
someone who hasn't taken the trouble to capitalise suitable words or use 
a spell-checker? I appreciate that English may not be your first 
language, but if you want free help, you need to make it easy for people 
to give it. That means constructing a sound description of your problem, 
and preferably think carefully about what you're doing in the first place.

Your topology is broken and you should work with tiny systems and 
simulate short periods until you work out what's wrong with it.

> here is my topology.
> thanx a lot in advance.
> ;topology file
> [ defaults ]
>  ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
>   2             1               no              1.0     
> 1.0                         
> [ atomtypes ]
> ;name        mass      charge   ptype            c6           c12
>    OX        15.99940     -1.30     A  2348.3193  0.0547148  51.712e-28
>    ZR        91.22420      2.70     A  0.0000000  0.0000000  0.0000000
> [ nonbond_params ]
>   ; i    j func           a             b    c6
>    OX   OX    2    2348.3193       0.0547148       51.712e-28
>    ZR    OX    2    9.512e+04       0.0376000       0.0000000
> ;   ZR   ZR    2    0.0000000       1.0000000       0.0000000
> [ moleculetype ]
>  ZR 3
>  
> [ atoms ]
>      1         ZR      1     DP     ZR      1      -1.3    91.22420
>  
> [ moleculetype ]
>  OX 3
>  
> [ atoms ]
>      1         OX      1     DP     OX      2       2.7    15.99940
>  
> [ system ]
> ZIRCONIA
>  
> [ molecules ]
> ZR  7932
> OX 15835  

For a start, what is the total charge of this system? Why do the charges 
of OX and ZR differ in different places? Why are there no Zr-Zr L-J 
interactions?

Mark