[gmx-users] NMA run problem

KARAKAS Esra Esra.Karakas at cea.fr
Thu Oct 8 13:08:09 CEST 2015

Dear Gromacs Users,

I am trying to run a Normal Mode Analysis with Gromacs v5.0.4 of a structure of 18081 atoms (without water) and I have a problem.
I did a several minimization of my structure (1 SD, 1 CD and 4 L-BFGS), and everything went well. You can see below the relative informations for my last L-BFGS minimization:

---------- At the top of my .log file:
Using 10 BFGS correction steps.

   F-max             =  9.76934e-06 on atom 15076
   F-Norm            =  7.50769e-07

---------- At the end of my .log file:
Low-Memory BFGS Minimizer converged to Fmax < 1e-07 in 132449 steps
Potential Energy  = -9.52896691013964e+04
Maximum force     =  9.82970751734797e-08 on atom 17063
Norm of force     =  1.69009515334513e-08

then, when I run my NMA, I see this message in my .log file:

Maximum force: 2.85412e+02
The force is probably not small enough to ensure that you are at a minimum.
Be aware that negative eigenvalues may occur
when the resulting matrix is diagonalized.

My command line is :
grompp_mpi_d -f nma.mdp -c em_BFGS_4_NoWater.gro -t em_BFGS_4_NoWater.trr -e em_BFGS_4_NoWater.edr -p protein.top -o nma_NoWater.tpr

My question is why I have such a large force ?

Thank you in advance for your help.

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