[gmx-users] system is exploding

Itamar Kass ikass at cc.huji.ac.il
Mon Sep 12 16:03:19 CEST 2005


Try some energy minimization after the insertion of the ion, or try some NVT md
steps.
 Cheers, Itamar.

Quoting taveechai taveecharoenkool <taweehui at yahoo.com>:

>
> dear all,
>  i have system contains proteins in hydrated popc
> bilayers. these proteins have a pore in the middle. i
> put one ion in the middle of the pore and then run md
> but at the step around 10,000 there are warning "
> system is exploding".  However, i ran this system
> (without ion) in 5ns and it doesn't have warnings.
> After i put ion , there are warning . How to do.
> thank you.
>
>
>
>
>
>
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===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Net: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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