[gmx-users] GROMACS 5 - problem with LINCS with freeze groups

[Tomek Wlodarski]

Hi Mark,

Thank you for replay.
I just checked this in Gromacs-4.6.7 and like you predicted I got same
LINCS warning.
I will fill bug report.
Best,

tomek

On Tue, Nov 11, 2014 at 1:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> You are using settings that trigger the group-scheme twin-range code.
> There's been a code bug there for a very long time, which we fixed after
> 4.6.5 (see http://redmine.gromacs.org/issues/1400. "Normal" usage such as
> in your .mdp file also tended to be broken when simulating water, which
> masked the code bug; your 4.6.5 run may look smooth, but probably the
> thermostat is hiding the systematic problem of nstlist*dt being too large
> to properly model water libration, and the symptoms of the virial problem
> we fixed are lost in the noise.
>
> If you can try 4.6.7, I expect that you will observe the same problems you
> see in 5.0.x. That will help us know what to consider fixing. We certainly
> didn't test the freeze-group functionality, so we could well have
> introduced a new problem, such as adding force components that were already
> zeroed for freezing. If I'm right about 4.6.7 also being broken, please
> file an issue at http://redmine.gromacs.org with a tarball of your grompp
> input files.
>
> Mark
>
> On Tue, Nov 11, 2014 at 2:05 PM, Tomek Wlodarski <
> tomek.wlodarski at gmail.com>
> wrote:
>
> > Hi,
> >
> > I experience some strange behaviour and I wonder if this is a bug or I am
> > doing something wrong.
> > I am running test simulation to check freeze groups in new gromacs.
> > And I am getting LINCS Warnings for atoms which should be frozen...:
> >
> > Step 0, time 0 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > rms nan, max inf (between atoms 30 and 31)
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >      32     33   90.8    0.1010  23.4699      0.1010
> >      32     34   90.3    0.1010  71.2488      0.1010
> > [...]
> >
> > my mdp file:
> >
> > ; RUN CONTROL PARAMETERS
> > integrator               = md
> > dt                       = 0.002   ; 2 femtosecond time step for
> > integration
> > nsteps                   = 500000  ; 1ns
> >
> > ; OUTPUT CONTROL OPTIONS
> > nstxout              = 5000    ; save coordinates every 2 ps
> > nstvout              = 5000    ; save velocities every 2 ps
> > nstenergy             = 5000    ; save energies every 2 ps
> > nstlog           = 5000    ; update log file every 2 ps
> > energygrps           = Protein Non-Protein
> > nstxtcout                = 5000
> > xtc-grps                 = non-Water
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > nstlist                  = 5
> > ns-type                  = Grid
> > cutoff-scheme            = group
> > pbc                      = xyz
> > rlist                    = 0.9
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > coulombtype              = pme
> > rcoulomb                 = 0.9
> > fourierspacing       = 0.12
> > ewald_rtol         = 1e-5
> > fourier_nx               = 0
> > fourier_ny               = 0
> > fourier_nz               = 0
> > optimize_fft         = yes
> > vdw-type                 = Cut-off
> > rvdw                     = 1.2
> > energygrp_table         =
> >
> > ; Temperature coupling
> > Tcoupl                   = V-rescale
> > tc-grps                  = Protein    Non-Protein
> > tau_t                    = 0.1        0.1
> > ref_t                    = 300        300
> >
> > ; Freeze atoms
> > freezegrps               = Protein
> > freezedim                = Y Y Y
> > energygrp-excl           = Protein Protein
> >
> > ; Pressure coupling
> > pcoupl                   = no
> >
> > ;Velocity generation
> > gen_vel          = no
> > gen_temp         = 300
> > gen_seed         = -1
> >
> > ;Constrain all bonds
> > constraints         = all-bonds
> > constraint-algorithm     = Lincs
> > lincs_iter              = 2             ; accuracy of LINCS
> > lincs_order          = 6            ; also related to accuracy
> >
> > Exactly the same system with the same mdp file I am running in Gromacs
> > 4.6.5 and everything runs smoothly.
> > Any suggestions?
> > Thanks a lot!
> > Best
> >
> > tomek
> > --
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