[gmx-users] Problems with Energy Minimization in Solvated Ligand

Toan Nguyen toan.nguy at berkeley.edu
Fri Dec 29 02:40:37 CET 2017


I am currently following the Gromacs Tutorial by Bevan Lab (Link
to run a simulation on a ligand from the 1mnb protein. However, I am
running into issues with the energy minimization step where I run *gmx
mdrun -v -nt 1 -deffnm em*, but an error arises saying,

*"WARNING: Listed nonbonded interaction between particles 1 and 119*
*at distance 2.108 which is larger than the table limit 2.000 nm.*

*This is likely either a 1,4 interaction, or a listed interaction inside*
*a smaller molecule you are decoupling during a free energy calculation.*
*Since interactions at distances beyond the table cannot be computed,*
*they are skipped until they are inside the table limit again. You will*
*only see this message once, even if it occurs for several interactions.*

*IMPORTANT: This should not happen in a stable simulation, so there is*
*probably something wrong with your system. Only change the table-extension*
*distance in the mdp file if you are really sure that is the reason."*

and then energy minimization runs for ~120 steps before saying,

*"Energy minimization has stopped, but the forces have not converged to the*
*requested precision Fmax < 100 (which may not be possible for your
*It stopped because the algorithm tried to make a new step whose size was
*small, or there was no change in the energy since last step. Either way,
*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.*

*writing lowest energy coordinates.*

*Steepest Descents converged to machine precision in 94 steps,*
*but did not reach the requested Fmax < 100.*
*Potential Energy  = -1.4016720e+05*
*Maximum force     =  1.9569155e+03 on atom 259*
*Norm of force     =  9.6724640e+01"*

When I do the tutorial with the provided input files, this message does not
show up and the energy minimization reaches 500+ steps. How can I fix my
input files so that the energy minimization does not run into the problem

Below is the link to my input files:

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