[gmx-users] REMD: when it exchange the replica, it will be bombed!!

[Mark Abraham]

On 19/11/2011 1:49 PM, 杜波 wrote:
> dear teachear,
> i do remd in NPT,
> when it exchange the replica, it will be bombed!!
>
> step 4000000, will finish Wed Nov 23 23:21:34 2011
> Warning: 1-4 interaction between 1384 and 1396 at distance 140.157 
> which is larger than the 1-4 table size 20.895 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> -------------------------------------------------------
> Program mdrun_mpi_4.5.5, VERSION 4.5.5
> Source code file: nsgrid.c, line: 549
>
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> Variable ci has value 175. It should have been within [ 0 .. 168 ]
>
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>

Did you check out the information available for this issue there? Does 
your simulation even run without REMD?

Mark