[gmx-users] My problem about the job under bond constrain?

[Anton Feenstra]

Hanming wrote:

> Dear all,
> I have a molecule which has more than 20,000 atoms. I tried to do the
> simulation under bond constrain in order to use the long step. Firstly I
> minimised the initial model by em and md under low temperature. Then I did
> the md without constrain, it can run smoothly. But when I add the
> bond-constrain the LINCS-WARNING always comes out and the job crashed. How
> can I do then?

Can you do an EM with all bonds constrained?

Can you do MD with all bonds constrained at a normal timestep (2fs)?

Can you do MD without constraints at a timestep of 3 or 4 fs?

(Are you sure you only changed the option for bond constraints?
You can use gmxcheck -s1 topol1.tpr -s2 topol2.tpr to check.)


-- 
Groetjes,

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