[gmx-users] Issues with energy minimization of a membrane protein

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Mon Sep 16 11:39:50 CEST 2019

Dear all,

I am interested in carrying out a simulation of mPGES-1 protein (PDB id:
4yl3), which is a homotrimer. I am using POPC membrane; equilibrated for
100 ns for this purpose. I was able to align and insert the protein into
the membrane using lambada align and inflategro programs, respectively. I
was also able to solvate, delete the extra solvent molecules using perl
script as described in the KALP15 tutorial.
After adding ions, I tried to carry out energy minimization and got this
note along with a premature termination at step 14.
"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 em.gro to ./#em.gro.2#

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  =  2.4501964e+16
Maximum force     =            inf on atom 3999
Norm of force     =            inf
I tried to carry out NVT but received a warning that the potential energy
of the system was too high leading to the termination at step 0
"Fatal error:
Step 0: The total potential energy is 9.96795e+14, which is extremely high.
The LJ and electrostatic contributions to the energy are 9.96795e+14 and
-1.7601e+06, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology."
I tried incorporating "constraints = none" in the em.mdp and redoing the
steps, with no luck. Request you to help me resolve this issue.
Thank you in advance.


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