Re: Simulation crashes during annealing the reverted all-atom structure

From: Peter Freddolino (
Date: Sat Jul 13 2019 - 22:09:46 CDT

Hi Rabeta,
The best strategy when faced with this sort of error is usually to set the
dcd output frequency to 1 and then inspect what happens to the system just
before it is crashing. Likely the rbcg heuristics somehow created a bad
starting structure; by inspecting the trajectory it may become obvious what
is going on. If not, could I have a look at your input files?

On Fri, Jul 12, 2019 at 6:07 PM Rabeta Yeasmin <>

> Dear NAMD users,
> I have run some protein-lipid coarse grained simulation using NAMD, where
> I had used residue based coarse grained method. After running the
> simulation for a while, I tried to revert the last coarse-grained structure
> (without water and ions) to all-atom structure. I used the CGTools Plugin
> to revert the structure which went well. But I am facing problem while
> annealing the reverted all-atom structure (after solvated and ionized). I
> used the automatically generated annealing configuration file during the
> reverse process. The annealing file constrains energy minimization, heating
> the system and then cooling it. The problem is- after the minimization
> steps, the simulation always crashes saying ' Atoms moving too fast the
> simulation has become unstable'. And also I checked the trajectory, the
> system i.e atoms does not move at all during the minimization step.
> Can you please tell me what am I doing wrong?
> Thanks.
> Rabeta Yeasmin

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