[gmx-users] Error during grompp

[Yang Ye]

Running out of box is common and it actually doesn't because of PBC. You 
may just continue the simulation

For this fatal error, you shall refer to how you have created the first 
tpr file: which top file you have used.

On 7/17/2007 5:39 PM, 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)
>
>  
>
> 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/> 
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>