Thanks in advance for your help.
ERROR: Water molecule starting at atom 14394 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate.
I tried changing mdp file and re-running it. This error hasn't appeared for the earlier simulations done for the same protein. I am just using a different ligand now.
How to mitigate this error in Gromacs protein-ligand simulation when running nvt equilibrium step as per Justin's tutorial?
The topology file had to be generated properly, i.e., problem with the coordinates (itp file) . Used the regenerated file, that resolved the error.
I would suggest to first run energy minimization module (e.g., using Conjugate Gradient method or others available in Gromacs), then using the final minimized structure you can start standard MD simulations.
The error could happen because of the bad contacts between atoms (i.e., distance between them is too small) and the forces become too large, thus the numerical integrators fails (think, the velocities are updated according: v(dt/2) = v(0) + (dt/2) F(0)/m, where dt is the integration step size and F(0) is the force at previous iteration step, if F(0) is too large, then the velocity becomes to large, which is equivalently adding too much energy into the system in the form of kinetic energy. Of course, reducing time step would help, but it all depends on the product (dt/2)*F(0) at the end!)
I met the similar problem, could you give me some advice? I had check my topology file but found no mistake.
Bad contacts refer to atomic clashes that arise either due to an insufficient minimization or broken model physics that cause molecules to collide with
one another. So increase the number of minimization steps. If it is your modeled protein. Trying remodeling with some other tools.
Are you running in GPU? make sure the topology is fine and reduce the time step and increase the number of steps in minimisation
Still not resolved give the full command you used.
The problem has been resolved. Thanks to all for your answers.
@Yaojia Chen - regenerate your topology file, even I couldn't find any fault but the newly generated file worked. Sometimes some elements in the topology are not generated.
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