[gmx-users] parameter declaration

[David van der Spoel]

On Tue, 2004-06-08 at 13:32, herbst at fhi-berlin.mpg.de wrote:
> Hello all,
> 
> I have tried to declare bond parameters in my topology-file, e.g.
> [ bonds ]
> ;  ai    aj funct            b0              kb
>     1     2     1           1.330000e-01  4.184000e+05
> 
put in the parameters twice:
;  ai    aj funct            b0              kb
>     1     2     1           1.330000e-01  4.184000e+05   1.330000e-01  4.184000e+05
> 



> but when I try to generate a .tpr file with grompp I get a warning for
> every line of parameter declaration:
> 
> WARNING 1 [file "S.top", line 54]:
>   No default Bond types for perturbed atoms, using normal values
> 
> after a few warnings the program crashes.
> What have I done wrong??
> And another question:
> When I delete all parameters, the simulation works, but the molecule flies
> apart, as if no parameters were defined at all. Should the program not use
> the parameters out of the .itp file in this case??
> 

you probably get a warning for missing parameters in that case
> Thanks,
> Anna
> 
> 
> 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++