[gmx-users] Error during grompp

[David van der Spoel]

Yulia Einav wrote:
>  
> Dear Gromacs users,
>  
> During my last simulation of 2 ns a part of a protein moved out of the water box. When I've tried to proceed to the next 2 ns I've got the folowing message during grompp:
>  
> Fatal error:
> 
> number of coordinates in coordinate file (wt_md2_egf4.gro, 17346)
> 
> does not match topology (topol.top, 0)
> 

there is something wrong in your topology. check manual chapter 5 and 
error messages from grompp.

>  
> 
> Furthemore the same part of the protein always move out of the box in different simulations.
> 
> Is there any way to prevent the moving? 
> 
> How do I continue the simulation from this point?
> 
>  
> 
> Thank you for your help,
> 
> Yulia
> 
> Yulia Einav Ph.D. 
>  
> Mathematical Biology Unit
> Department of Applied Mathematics
> Faculty of Sciences, H.I.T. 
> 52 Golomb Str. POB 305, Holon 58102, Israel.
> Tel. 972-3-5026769, Fax. 972-3-5026619. 
> E-mail: yulia_e at hit.ac.il, Web: http://www.hit.ac.il <http://www.hit.ac.il/> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se