[gmx-users] em error

[Anton Feenstra]

Arturas wrote:

> Hi,
> 
> I've modified HEME with indtroduction of oxygen bound to Fe.
> After energy minimisatio heme's Fe atom moves out of plain and
> something wrong gets with energies (below).
> 
> What should be corrected ?

Things to check:
- what happens to the conformation? Try nstxtcout=1 to get all EM
steps as frames in the .xtc file.
- what charges did you put on Fe and oxygens?
- did you add bonds, angles and dihedrals?
- where did you get bond lengths, angles and forceconstants?
- did you add exclusions as well?
- did you check which energy terms go 'off' first? These you should
find in the .log file, or else run the EM again with nstener=1 so you
get all energy terms in the .edr file.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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