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

From: Peter Freddolino (
Date: Wed Jul 24 2019 - 00:17:22 CDT

Hi Rabeta,
It is impossible for me to be sure what is going on without seeing the
structures - are you able to send those as well?

On Tue, Jul 23, 2019 at 12:43 PM Rabeta Yeasmin <>

> Hi Peter,
> Sorry for the late reply. I have checked the trajectory, it looks like
> some of the bonds are stretched in the original structure i.e rbcg created
> a bad structure. But I am not sure how to avoid this kind of problem. I
> have attached the input files for annealing here.
> Thank so much for your time.
> Rabeta Yeasmin
> On Sat, Jul 13, 2019 at 10:08 PM Peter Freddolino <>
> wrote:
>> 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?
>> Thanks,
>> Peter
>> On Fri, Jul 12, 2019 at 6:07 PM Rabeta Yeasmin <>
>> wrote:
>>> 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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