[gmx-users] strange behavior during energy minimization

Gergely Gyimesi gergely.gyimesi at ibmm.unibe.ch
Wed May 17 19:55:41 CEST 2017


Dear Gromacs users,

I get strange behavior when trying to energy minimize a frame from a 
simulation. I'm probably overlooking some settings, but I would 
appreciate any advice.

I have a membrane protein system prepared using CHARMM-GUI of about 80k 
atoms (CHARMM36 ff, TIP3 water). I'm using gromacs 2016 on a GPU 
workstation. Equilibration and a production run of 1 ns (500k steps) 
went without errors.

Now I am trying to energy minimize a selected frame from the simulations 
using double-precision gromacs 2016. I usually like to set 
constraints=none for this (see full mdp file below). At first I was 
trying with integrator=cg, but I got an error saying "step -1: One or 
more water molecules can not be settled." (see output below). I saw in 
the manual that constraints=none means "No constraints except for those 
defined explicitly in the topology", which I find somewhat 
counterintuitive, so my first question is, is it possible to completely 
disable all constraints for a run?

Afterwards I tried the same mdp file with integrator=steep, in which 
case the EM got stuck at an Fmax value around 1e3-1e4 at a specific atom 
27434 (see output below) and could not further minimize. Checking the EM 
trajectory, atom 27434 belongs to a lipid molecule and its bond length 
seems to fluctuate around a specific value without ever reaching an EM 
state. It seemed like constraints are still acting but failing to 
normalize the geometry for some reason. This was also strange because as 
far as I could see, lipid molecules have no constraints defined in their 
topologies and constraints was set to "none".

I have checked the 1 ns production trajectory and the input frame for 
the EM and I don't see any obvious distortions near atom 27434, so I'm 
pretty sure that my system is not blowing up.

Is there anything else to check why I get this behavior, or is it an 
obvious problem and I'm overlooking some settings?

Thanks for any help,
Gergely Gyimesi



MDP FILE USED:

integrator              = cg
emtol                   = 100.0
nsteps                  = 1000

cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2

tcoupl                  = no
pcoupl                  = no

constraints             = none
lincs-iter              = 8

OUTPUT OF CG EM:

Polak-Ribiere Conjugate Gradients:
    Tolerance (Fmax)   =  1.00000e+02
    Number of steps    =         1000
    F-max             =  5.64020e+03 on atom 767
    F-Norm            =  7.18633e+02

Step 0, Epot=-7.012054e+05, Fnorm=6.979e+02, Fmax=5.307e+03 (atom 767)
Step 1, Epot=-7.042373e+05, Fnorm=6.663e+02, Fmax=4.805e+03 (atom 767)
Step 2, Epot=-7.084643e+05, Fnorm=6.225e+02, Fmax=4.117e+03 (atom 767)
Step 3, Epot=-7.142353e+05, Fnorm=5.635e+02, Fmax=3.284e+03 (atom 25370)
Step 4, Epot=-7.215553e+05, Fnorm=4.924e+02, Fmax=2.813e+03 (atom 25370)
Step 5, Epot=-7.302426e+05, Fnorm=4.184e+02, Fmax=2.204e+03 (atom 25370)
Step 6, Epot=-7.402236e+05, Fnorm=3.538e+02, Fmax=1.563e+03 (atom 21300)
Step 7, Epot=-7.519179e+05, Fnorm=3.026e+02, Fmax=1.279e+03 (atom 79282)
Step 8, Epot=-7.658784e+05, Fnorm=2.572e+02, Fmax=1.066e+03 (atom 79282)

step -1: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

-------------------------------------------------------
Program:     gmx mdrun, version 2016
Source file: src/gromacs/mdlib/minimize.cpp (line 718)
MPI rank:    1 (out of 2)

Fatal error:
The coordinates could not be constrained. Minimizer 'cg' can not handle
constraint failures, use minimizer 'steep' before using 'cg'.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

OUTPUT OF STEEP EM:

Steepest Descents:
    Tolerance (Fmax)   =  1.00000e+02
    Number of steps    =         1000
Step=    0, Dmax= 1.0e-02 nm, Epot= -6.99201e+05 Fmax= 5.64020e+03, 
atom= 767
Step=    1, Dmax= 1.0e-02 nm, Epot= -7.33998e+05 Fmax= 7.17997e+03, 
atom= 15789
Step=    2, Dmax= 1.2e-02 nm, Epot= -7.47185e+05 Fmax= 1.08109e+04, 
atom= 18684
Step=    3, Dmax= 1.4e-02 nm, Epot= -7.57996e+05 Fmax= 9.93073e+03, 
atom= 18684
Step=    4, Dmax= 1.7e-02 nm, Epot= -7.62278e+05 Fmax= 1.58000e+04, 
atom= 18684
Step=    5, Dmax= 2.1e-02 nm, Epot= -7.70503e+05 Fmax= 1.43830e+04, 
atom= 18684
Step=    7, Dmax= 1.2e-02 nm, Epot= -7.80685e+05 Fmax= 3.94937e+03, 
atom= 18684
Step=    8, Dmax= 1.5e-02 nm, Epot= -7.85390e+05 Fmax= 1.72944e+04, 
atom= 18684
Step=    9, Dmax= 1.8e-02 nm, Epot= -7.94384e+05 Fmax= 9.02707e+03, 
atom= 18684
Step=   11, Dmax= 1.1e-02 nm, Epot= -7.98235e+05 Fmax= 6.65069e+03, 
atom= 24559
Step=   12, Dmax= 1.3e-02 nm, Epot= -7.99736e+05 Fmax= 1.24235e+04, 
atom= 18684
Step=   13, Dmax= 1.5e-02 nm, Epot= -8.03474e+05 Fmax= 1.02483e+04, 
atom= 24559
Step=   15, Dmax= 9.3e-03 nm, Epot= -8.07510e+05 Fmax= 3.45981e+03, 
atom= 24559
Step=   16, Dmax= 1.1e-02 nm, Epot= -8.09423e+05 Fmax= 1.28959e+04, 
atom= 24559
Step=   17, Dmax= 1.3e-02 nm, Epot= -8.13783e+05 Fmax= 6.81833e+03, 
atom= 24559
Step=   19, Dmax= 8.0e-03 nm, Epot= -8.15942e+05 Fmax= 5.03772e+03, 
atom= 12800
Step=   20, Dmax= 9.6e-03 nm, Epot= -8.17276e+05 Fmax= 9.03983e+03, 
atom= 12800
Step=   21, Dmax= 1.2e-02 nm, Epot= -8.19280e+05 Fmax= 8.20369e+03, 
atom= 12800
Step=   22, Dmax= 1.4e-02 nm, Epot= -8.19682e+05 Fmax= 1.21629e+04, 
atom= 12800
Step=   23, Dmax= 1.7e-02 nm, Epot= -8.21166e+05 Fmax= 1.26228e+04, 
atom= 12800
Step=   25, Dmax= 1.0e-02 nm, Epot= -8.24889e+05 Fmax= 2.01639e+03, 
atom= 12800
Step=   26, Dmax= 1.2e-02 nm, Epot= -8.26366e+05 Fmax= 1.59595e+04, 
atom= 12800
Step=   27, Dmax= 1.4e-02 nm, Epot= -8.31138e+05 Fmax= 5.10635e+03, 
atom= 12800
Step=   29, Dmax= 8.6e-03 nm, Epot= -8.31982e+05 Fmax= 7.73469e+03, 
atom= 12800
Step=   30, Dmax= 1.0e-02 nm, Epot= -8.33111e+05 Fmax= 7.45970e+03, 
atom= 12800
Step=   31, Dmax= 1.2e-02 nm, Epot= -8.33368e+05 Fmax= 1.09873e+04, 
atom= 12800
Step=   32, Dmax= 1.5e-02 nm, Epot= -8.34397e+05 Fmax= 1.09141e+04, 
atom= 12800
Step=   34, Dmax= 8.9e-03 nm, Epot= -8.36805e+05 Fmax= 2.39162e+03, 
atom= 12800
Step=   35, Dmax= 1.1e-02 nm, Epot= -8.37508e+05 Fmax= 1.33026e+04, 
atom= 12800
Step=   36, Dmax= 1.3e-02 nm, Epot= -8.40119e+05 Fmax= 5.86465e+03, 
atom= 12800
Step=   38, Dmax= 7.7e-03 nm, Epot= -8.40984e+05 Fmax= 5.47169e+03, 
atom= 12800
Step=   39, Dmax= 9.3e-03 nm, Epot= -8.41539e+05 Fmax= 8.29082e+03, 
atom= 12800
Step=   40, Dmax= 1.1e-02 nm, Epot= -8.42365e+05 Fmax= 8.04508e+03, 
atom= 12800
Step=   41, Dmax= 1.3e-02 nm, Epot= -8.42464e+05 Fmax= 1.17453e+04, 
atom= 12800
Step=   42, Dmax= 1.6e-02 nm, Epot= -8.43201e+05 Fmax= 1.17935e+04, 
atom= 12800
Step=   44, Dmax= 9.6e-03 nm, Epot= -8.45204e+05 Fmax= 2.49172e+03, 
atom= 12800
Step=   45, Dmax= 1.2e-02 nm, Epot= -8.45528e+05 Fmax= 1.44115e+04, 
atom= 12800
Step=   46, Dmax= 1.4e-02 nm, Epot= -8.47770e+05 Fmax= 6.17261e+03, 
atom= 12800
Step=   48, Dmax= 8.3e-03 nm, Epot= -8.48428e+05 Fmax= 6.01655e+03, 
atom= 12800
Step=   49, Dmax= 1.0e-02 nm, Epot= -8.48835e+05 Fmax= 8.75001e+03, 
atom= 12800
Step=   50, Dmax= 1.2e-02 nm, Epot= -8.49445e+05 Fmax= 8.81038e+03, 
atom= 12800
Step=   51, Dmax= 1.4e-02 nm, Epot= -8.49487e+05 Fmax= 1.24344e+04, 
atom= 12800
Step=   52, Dmax= 1.7e-02 nm, Epot= -8.49988e+05 Fmax= 1.28654e+04, 
atom= 12800
Step=   54, Dmax= 1.0e-02 nm, Epot= -8.51787e+05 Fmax= 2.47881e+03, 
atom= 12800
Step=   55, Dmax= 1.2e-02 nm, Epot= -8.51916e+05 Fmax= 1.57155e+04, 
atom= 12800
Step=   56, Dmax= 1.5e-02 nm, Epot= -8.53974e+05 Fmax= 6.40033e+03, 
atom= 12800
Step=   58, Dmax= 8.9e-03 nm, Epot= -8.54481e+05 Fmax= 6.70575e+03, 
atom= 12800
Step=   59, Dmax= 1.1e-02 nm, Epot= -8.54805e+05 Fmax= 9.14479e+03, 
atom= 12800
Step=   60, Dmax= 1.3e-02 nm, Epot= -8.55241e+05 Fmax= 9.83986e+03, 
atom= 27434
Step=   61, Dmax= 1.5e-02 nm, Epot= -8.55311e+05 Fmax= 1.31050e+04, 
atom= 27434
Step=   62, Dmax= 1.9e-02 nm, Epot= -8.55622e+05 Fmax= 1.42933e+04, 
atom= 27434
Step=   64, Dmax= 1.1e-02 nm, Epot= -8.57267e+05 Fmax= 2.28255e+03, 
atom= 27434
Step=   65, Dmax= 1.3e-02 nm, Epot= -8.57613e+05 Fmax= 1.75755e+04, 
atom= 27434
Step=   66, Dmax= 1.6e-02 nm, Epot= -8.59394e+05 Fmax= 6.35274e+03, 
atom= 27434
Step=   68, Dmax= 9.6e-03 nm, Epot= -8.59780e+05 Fmax= 7.87227e+03, 
atom= 27434
Step=   69, Dmax= 1.2e-02 nm, Epot= -8.60142e+05 Fmax= 9.23701e+03, 
atom= 27434
Step=   70, Dmax= 1.4e-02 nm, Epot= -8.60431e+05 Fmax= 1.12330e+04, 
atom= 27434
Step=   71, Dmax= 1.7e-02 nm, Epot= -8.60665e+05 Fmax= 1.34196e+04, 
atom= 27434
Step=   72, Dmax= 2.0e-02 nm, Epot= -8.60799e+05 Fmax= 1.60503e+04, 
atom= 27434
Step=   74, Dmax= 1.2e-02 nm, Epot= -8.62094e+05 Fmax= 1.77170e+03, 
atom= 27434
Step=   75, Dmax= 1.4e-02 nm, Epot= -8.63196e+05 Fmax= 1.96982e+04, 
atom= 27434
Step=   76, Dmax= 1.7e-02 nm, Epot= -8.64552e+05 Fmax= 6.06436e+03, 
atom= 27434
Step=   78, Dmax= 1.0e-02 nm, Epot= -8.64872e+05 Fmax= 9.23615e+03, 
atom= 27434
Step=   79, Dmax= 1.2e-02 nm, Epot= -8.65232e+05 Fmax= 9.15751e+03, 
atom= 27434
...


-- 
Gergely Gyimesi, PhD
Postdoctoral Research Fellow
Institute of Biochemistry and Molecular Medicine
University of Bern
Bühlstrasse 28
CH-3012 Bern     | phone: +41 (0)31 631 4739
Switzerland      | mailto:gergely.gyimesi at ibmm.unibe.ch



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