Simulation crashes during annealing the reverted all-atom structure

From: Rabeta Yeasmin (
Date: Fri Jul 12 2019 - 16:11:25 CDT

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?

Rabeta Yeasmin

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