[gmx-users] amyloid simulation in water+glucose

[Anton Feenstra]

Aswin Narain wrote:
> Hi all
> 
> As a relative new-bie to gromacs I did not really
> understand the reply. But then, the energy
> minimization that I tried was a flop as well. The
> result was: converged to machine precision. Step size
> too small. 
> A more detailed answer will be really helpful!

'converged to machine precision' is not a flop per se! Check what your
actual maximum force was at the last step (mdrun will have printed that
on your screen as well as in the .log file) and compare to the setting
you had in your .mdp file. It may be already close. I can generally
minimize a protein structure to a maximum force of around 1000 (i.e.,
sometimes I reach 4000, sometimes 700, both I consider good results).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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