[gmx-users] My problem about the job under bond constrain?
feenstra at chem.vu.nl
Wed Sep 1 17:20:40 CEST 2004
> 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.)
| | |
| _ _ ___,| 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/ |
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