[gmx-users] setting up forcefield

[K.A.Feenstra]

saicheong chung wrote:
> 
> Dear all,
> 
> I tried to run a simulation of the polymer with
> SHAKE-fixed bond/angles.  Taking into account
> only the dihedrals, charge and LJ forces.  I
> want to use a non-default forcefield taking from
> a publication.
> 
> I somehow managed to take the trouble of mimicing the
> ffgmx forcefield and created the corresponding files
> in the "top" directory.  And pdb2gmx and grompp are
> able to generate the tpr file.  However, there must
> be something wrong that my molecule is alway exploding
> and got the "shake error".   I am at lost where to
> look now.  Would you please give me some tips?

My first gues would be an error in your topology. We don't have many
programs in Gromacs that can help you check them. However, you can
start with ngmx, which will display bonds as you have defined them.

Next, you could try my simple topology parsing script, which I posted
to this list some days ago...

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | Anton Feenstra       Dept. of Biophysical Chemistry |
|  _   _  ___,| K.A.Feenstra at chem.rug.nl    University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327                    Nijenborgh 4 |
|(   |   )| | | Fax +31 50 363 4800               9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton        The Netherlands |
|             | "The Wheels On the Bus Go Round and Round" (J. Richm|
|_____________|_____________________________________________________|