[gmx-users] Segmentation fault 3

[Anton Feenstra]

Christoph Freudenberger wrote:
> Tanos C. C. França wrote:
>>
>>             I am facing the problem of segmentation fault again 
>> !!!!!!!!!!!! This time I am trying to perform a Position Restrained 
>> (PR) molecular dynamics (MD) of a crystallographic structure I have 
[...]
> You're using
> constraints         =  all-bonds
> with the default LINCS algorithm. Looks like your system gives coupled
> constraints that cannot be resolved by LINCS (check the manual about that).

If it's just a protein, all-bonds & Lincs should work.
Perhaps there are strange things in your crystal structure.
Did you do EM before the MD? (You *must*!)
Have you checked the crystal structure with for example ProCheck?


-- 
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)                               |
|_____________|_______________________________________________________|