I'm trying to do SMD via NAMD, pulling one protein dimer away from another dimer. However, when I fix some of the atoms of the static dimer, and try to pull the other dimer away with constant velocity, I face the Error below:
Constraint failure in RATTLE algorithm for atom 5380!
(each time for a different atom)
I initially minimized my system for 4000 timesteps and then increased the minimization steps to 10000 and then let the system be in equilibrium for 0.1 ns, but the problem still shows up when trying to do SMD.
My time step is set to 1 fs which is small enough.
It is notable that the simulation runs without error when none of the atoms are fixed and no constraint is applied to smd atoms. but in that case, the first dimer will follow the second dimer which is pulled.
Can anyone gives a hint which might be wrong in fixing the atoms?
Dear Mahya,
It may also be that you are pulling too quickly. What are you using for smdVel? Can you try reducing it? What if you fix the atoms but turn SMD off.
Jeff
can you tell me what will be the script for the energy minimization and equilibration of your dimer protein?
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