peptid bond omega, problems with settings?

From: Hua Wong (
Date: Fri Apr 16 2004 - 09:25:22 CDT

>Just a few comments:
>First, is your box size the same size or larger than your cutoffs?
>Second, pulsing your system with 300K worth of energy all at once may
>create some unpleasant results. Equilibration/slow heating might help.

Will check...

>Finally, what does the energy of the minimized system look like?
>400 steps seems a wee bit short unless you have a small system.

And the 400 steps is a nitwit error. I got confuse with all the .namd file I have.
In fact I make multiple minimizations of 1000 to 2000 steps. Taking the .coor output as an input for the next minimization.

System is big enough, 336 residue.

As far as my limited knowledge helps, I think energy value is correct. The whole energy goes quickly from high positiv value (99999999.9999) down to high negativ value (-17037.2175) stable at half the minimization.

One annoying fact is that the dihedral grows all along and stabilises at half the minimization. On the contrary, angle goes down.

If it doesn't help, feel free to ask more details



|Wong Hua |
|Student |
|Equipe de Bioinformatique Génomique et Moléculaire |
|INSERM, E03-46, Université Paris 7, case 7113, |
|2, place Jussieu, 75251 Paris Cedex 05 - FRANCE |

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