[gmx-users] problem with center of mass removal, rest-group, all gmx versions

[David van der Spoel]

Michael Brunsteiner wrote:
> 
> Hi everybody,
> 
> Trying to simulate a solvated protein/ligand complex
> my system keeps blowing up with lincs errors after some
> un-predictible amount of simulation time (anything between
> 10 and 1000 ps) i tried out numerous combinations of
> mdp settings/parameters and gromacs versions, and nothing
> seems to help, but there is one point that's still unclear
> and I wonder whether this can be the problem:
> In ALL my md.log files is see the following output:
> 
> We have the following groups for center of mass motion removal:
>   0:  rest, initial mass: 163113
> There are: 6508 Atoms
If your system contains 6508 this is the whole system and that should 
not be the cause of the lincs problem.
> 
> in the mdp-documentation it says:
> 
> comm_grps:
>     group(s) for center of mass motion removal, default is the whole system
> 
> I only now noticed that i never set comm_grps explicitly,
> assuming that the default (System) is ok, the comm_mode i typically
> set to Linear and nst_comm to either 100 or 1, or I leave these
> commands out altogether assuming that the defaults are ok ...
> system blows up in each case.
> My system has much more than 6508 atoms, and none of the groups in the
> ndx file contains 6508 atoms, and i double and triple checked that
> there is not a sigle atom that is NOT member of some group in the
> ndx file ... so what is this "rest" group??  it is apparently
> made automatically by grompp or mdrun. I can imagine that constraining
> the center of mass of a (possibly randomly chosen) subgroup of
> atoms can cause instabilities, has anybody observed something
> like this before ??
> I have seen a couple of mails in this list in which people describe
> similar problems, but found none with a solution/explanation.
> 
> I should add that i run gromcas on an AMD64 PC,
> linux 2.6.9. I also tried a 32 bit machine, and I tried gmx 3.3.2,
> 3.3.3, 4.0 and 4.0.2 ... always the same problem.
> 
> any help is appreciated! (sample mdp file below)
> 
> cheers,
> Michael
> 
> 
> 
> mdp-file (please mind that this is just one example,
> i tried out many modifications of practically every
> single parameter that might cause the problem, tried shake
> varied lincs_iter, thermostate, etc...)
> 
> cpp                      = /usr/bin/cpp
> ;
> integrator               = md
> nsteps                   = 500000
> dt                       = 0.002
> ;
> nstxtcout                = 1000
> xtc_grps                 = receptor ligand
> nstenergy                = 100
> nst_log                  = 100
> nstxout                  = 10000
> nstvout                  = 10000
> ;
> nstlist                  = 12
> nstype                   = grid
> pbc                      = xyz
> nstcomm                  = 100
> rlist                    = 1.2
> ;
> coulombtype              = PME
> rcoulomb                 = 1.2
> vdwtype                  = shift
> rvdw                     = 1.2
> ;
> tcoupl              =  Berendsen
> tc-grps             =  System
> ref_t               =  300
> tau_t               =  0.1
> ;
> Pcoupl                   = no
> ;
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = no
> fourier_nx               = 32
> fourier_ny               = 32
> fourier_nz               = 32
> ;
> constraints              = all-bonds
> unconstrained-start      = no
> lincs_iter               = 8
> ;
> energygrps               = receptor ligand solvent
> 
> 
>       
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se