[gmx-users] Protein breaking apart in implicit solvent MD simulations using GROMACS

[Baswanth Oruganti]

Dear all,

I have been trying to perform implicit solvent MD simulations on a Kinase
protein. Gromacs is crashing with several LINCS warnings such as one shown
below. When I visualize output with vmd, I see that some atoms move very
large distances and finally protein is breaking apart.

Before the production MD run, I did energy minimization and a
position-restraint equilibration with a smaller time step than that of
production run. The starting configurations for the energy minimization are
taken from EDS sampling of a 50 ns trajectory run in explicit solvent.
Energy minimization output is also shown below.

I am also attaching the .mdp files I used for E minimization (em.mdp),
position-restraint equilibration (pr.mdp) and production MD run
(implicit.mdp). Could you suggest me ways to troubleshoot this issue?

Error:












* "Step 6907, time 6.907 (ps)  LINCS WARNING relative constraint deviation
after LINCS: rms 0.000588, max 0.013660 (between atoms 1581 and 1583) bonds
that rotated more than 30 degrees:  atom 1 atom 2  angle  previous,
current, constraint length    1591   1593   36.0    0.1346   0.1716
0.1345    1593   1594   42.9    0.0998   0.1386      0.0997    1593
1595   80.9    0.1437   0.2152      0.1430    1595   1596   87.0
0.1085   0.1613      0.1080    1595   1597  117.2    0.1549   0.1864
0.1538    1595   1615   68.1    0.1494   0.2074      0.1490" * Energy
Minimization output:
Steepest Descents converged to Fmax < 100 in 3065 steps
Potential Energy  = -1.7024426e+04
Maximum force     =  9.9019478e+01 on atom 3520
Norm of force     =  1.2291615e+01

Thanks & Regards,
Baswanth.

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