check your custom topology (this is where the error is 99% of the time),
use qm minimized starting structures, make sure your structure matches
your topology (atom names,numbers,ordering, etc.), test single molecules
in vacuum first and/or reduce the step size of your SD minimizer.
On 11/26/2010 11:47 AM, Baofu Qiao wrote:
If you are really sure about the topology, the problem is the initial
structure. Try to use PackMol to build it.
On 11/26/2010 11:42 AM, Olga Ivchenko wrote:
I tried today to run minimization in vacuum for my small molecules. This has
the same error.
2010/11/26 Baofu Qiao<qia...@gmail.com>
Have you run the energy minimization (or further simulation to optimize
the structure and test the FF) on the small molecule before you added it
into water?
On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
Dear gromacs users,
I am trying to run simulations for small molecules in water. Topology
files
I created by my self for charm ff. When I am trying to start energy
minimization I got an error:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 1000
That's means my system is exploding. Please can you advice me on this,
what
I need to check.
best,
Olga
--
************************************
Dr. Baofu Qiao
Institute for Computational Physics
Universität Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Tel: +49(0)711 68563607
Fax: +49(0)711 68563658
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