NAMD Simulation error

From: Anirban Ghosh (anirbang_at_cdac.in)
Date: Fri Nov 14 2008 - 02:36:16 CST

>
> Hi ALL,
>
> I am running a simulation of a residue based CG model of 856 CG beads in
> NAMD. I am running it using implicit solvent condition without PBC and
> PME. After 5000 steps of minimization the system ran for 550000 steps and
> gave a error:
> ------------------------------------------------------------
> FINISHED WRITING RESTART VELOCITIES
> LDB: LOAD: AVG 0.110926 MAX 0.150218 MSGS: TOTAL 38 MAXC 7 MAXP 7 None
> LDB: LOAD: AVG 0.110926 MAX 0.112707 MSGS: TOTAL 38 MAXC 7 MAXP 7
> Refine
> ERROR: Atom 744 velocity is 684.102 -844.858 588.241 (limit is 1000)
> ERROR: Atom 750 velocity is -555.261 769.693 -387.632 (limit is 1000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Exiting prematurely.
> ==========================================
> WallClock: 929.760376 CPUTime: 643.129211 Memory: 7608 kB
> -------------------------------------------------------------
>
> In the error the atom velocities did not cross 1000 (which is shown to be
> the limit) but still it terminated. I am getting the same error but at a
> very early stage if I use PBC and PME. I have tried increasing the box
> size also and now without PBC, but every time I am getting this error. The
> configuration script is attached. Please suggest a solution. Thanks
>
> Regards,
>
> --
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Scientific & Engineering Computing Group
> Centre for Development of Advanced Computing
> Pune, India
>
>
>

-- 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

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