Hi, I am roughly following this tutorial
https://github.com/LHRK/Nanodisc-Builder
to create a nanodisc surrounded by an APOA1 protein. I have completed the initial steps and am now starting minimization, but receive many LINCS errors and this error:
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 10 (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.
I have tried a variety of different minimization parameters but all have led to the same error (tcoupling, no lincs parameters, added constraints etc.)
When I try to do an NVT equilibration, it states that the energy is too high to run, showing that the original file does have too much energy.
Here is my current minimization.mdp:
integrator = steep
dt = 0.01
nsteps = 50000
nstcomm = 100
comm-grps =
lincs-order = 8
lincs-iter = 1
lincs-warnangle = 360
constraints = none
cutoff-scheme = Verlet
rlist = 1.2
rvdw = 1.2
coulombtype = PME
fourierspacing = 0.3
rcoulomb = 2.5
and attached is the starting file. Does anyone have suggestions on how to edit the minimization or fix the gro file if this is the issue>
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