GROMACS version: Latest
GROMACS modification: Yes/No
Here post your question
I am simulating a peptide in lipid bilayer and construct the initial structure in CHARMM-GUI.
I followed standard files given by charmm-gui. But while energy minimization it shows error.
Below i am attaching mdp file and detailed comments after the energy minimization in gromacs.
define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
integrator = steep
emtol = 1000.0
nsteps = 50000
emstep = 0.01 ; Minimization step size
nstlist = 20
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = pme
rcoulomb = 1.2
;
constraints = h-bonds
constraint_algorithm = LINCS
COMMENTS-
step -1, time -0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000400, max 0.010753 (between atoms 12117 and 12116)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
Back Off! I just backed up step6.0_minimization.trr to ./#step6.0_minimization.trr.3#
Back Off! I just backed up step6.0_minimization.edr to ./#step6.0_minimization.edr.3#
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 2.78783e+16 Fmax= inf, atom= 14472
Step= 14, Dmax= 1.2e-06 nm, Epot= 5.69698e+16 Fmax= inf, atom= 14470
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 1000 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.
Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Back Off! I just backed up step6.0_minimization.gro to ./#step6.0_minimization.gro.3#
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 2.7878276e+16
Maximum force = inf on atom 14472
Norm of force = inf
NOTE: 16 % of the run time was spent in domain decomposition,
10 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
gcq#0: “If You Want Something Done You Have to Do It Yourself” (Highlander II)