Gromacs molecular dynamics simulation with three ligands stops at equilibration. Outpu is:
starting mdrun 'Protein in water'
50 steps, 0.1 ps.
step 0
Step 3, time 0.006 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 20889.980469, max 550719.500000 (between atoms 3117 and 3118)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3117 3118 107.2 0.1000 55072.0547 0.1000
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
I think there is a problem with starting geometry and the energy minimization step was not also properly conversed! Probably bad contacts are there in the initial geometry. How did you choose your ligands positions? Did you dock the ligands or manually placed at arbitrary positions?
What is happening in your system is independent if you have 1, 2 or more ligands, what the error described by gromacs tells you is that the bond between these two atoms (3117 and 3118) is separating, for some reason. What you must do is look at which these two atoms are (according to the .gro file) and see in the topology if everything is well defined, so that the parameters are not responsible for the opening (misallocation or lack of allocation of angles or dihedral angles; or lack of assignment of the bond itself). If that's not the case, there is most likely an overlap of the van der Waals radii of two atoms, so you should have more equilibrium instances of the system. You can do this in a number of different ways: you can either perform more energy minimization steps or perform NVT and / or NPT steps with smaller dts and gradually increase the dt, up to 1 fs.
Actually, your dt of 0.1 ps catches my eye (is your system coarse grained?), because ifnot, you are using an infeasible dt, the largest dt you can use in an atomistic or united-atom system is 1 fs (0.001 ps) or at least, 2fs if you use constraints with the LINCS algorithm.
In short, understanding what is happening in your system is a matter of strictly looking at the error that it indicates to you, in all the possible variables that may be the generators of the problem.
Regards
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