[gmx-users] Error during grompp

[Yulia Einav]

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/>