[gmx-users] mdrun error

[David]

On Sat, 2004-10-02 at 15:12, Hector Mrz-Seara Monne wrote:
> 
> spoel at xray.bmc.uu.se wrote:
> > On Sat, 2004-10-02 at 13:39, Hector Mrz-Seara Monne wrote:
> >   
> > > Hello All,
> > > 
> > > Maybe the question that follow has been posted before but I wasn't
> > > able to find it, then if anyone knows where just told me. My problem
> > > is that my monolayer system is working well, but after a 1.7 ns of
> > > dynamics with a step 1fs I get the following error:
> > > 
> > >     
> > Have you stopped the center of mass motion? Sometimes it ahs to be done
> > per group (e.g. monolayer and water).
> This simulation was made in vacuum. Only de monomer here is the *.top
> file:
> 
> #include "ffgmx.itp"
> #include "azo_neutral.itp"
>                                                                                                           
> [ system ]
> Neutral monomer Azobenzenos
>                                                                                                           
> [ molecules ]
> DRG      225
> 
> 
> 
> And the part corresponding to the removal of the translation of CM in
> the dyn.mdp is the following:
> 
> ; mode for center of mass motion removal
> comm-mode                = Linear
> ; number of steps for center of mass motion removal
> nstcomm                  = 1
> ; group(s) for center of mass motion removal
> comm-grps                =

OK that looks fine. Have you verified (md.log file) that these settings
have been incorporated in the tpr file?

Have you tried visualising the trajectory?

Do you have periodic boundary conditions? Otherwise you might want to
set comm-mode = angular

>                                                                                                           
> > Also your temperature is 450 K. Do you have T coupling turned on?
> I think that something is not working well since in the bath is set to
> 300 K, in fact I have not notice that before posting my report, as
> follow in the dyn.mdp:
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl                   = berendsen
> ; Groups to couple separately
> tc-grps                  = System
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.1
> ref_t                    = 300
> ; Pressure coupling
> Pcoupl                   = no
> Pcoupltype               = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> ; Random seed for Andersen thermostat
> andersen_seed            = 815131
>                                                                                                           
> Have you any sugestion? Thank you David
> > 
> >   
> > >        Step           Time         Lambda
> > >         1731000     1731.00012        0.00000
> > >                                                                                                           
> > >    Energies (kJ/mol)
> > >            Bond          Angle    Proper Dih.  Improper Dih.         
> > > LJ-14
> > >     3.07715e+04    6.36605e+03    2.02562e+03    1.27192e+03   
> > > 2.39194e+04
> > >      Coulomb-14        LJ (SR)        LJ (LR)  Disper. corr.   Coulomb
> > > (SR)
> > >    -4.35088e+03   -4.18427e+04   -3.79469e+03   -2.96826e+02  
> > > -1.61672e+04
> > >    Coulomb (LR)      Potential    Kinetic En.   Total Energy   
> > > Temperature
> > >     3.08142e+02   -1.78960e+03    3.78781e+04    3.60885e+04   
> > > 4.50009e+02
> > >  Pressure (bar)
> > >    -4.24753e+02
> > >                                                                                                           
> > > Large VCM(group rest):      0.00172,     -0.00977,     -0.00129,
> > > ekin-cm:  4.46633e+00
> > > Large VCM(group rest):      0.00213,     -0.00449,      0.00016,
> > > ekin-cm:  1.10213e+00
> > > Large VCM(group rest):      0.00437,     -0.00540,     -0.00333,
> > > ekin-cm:  2.64588e+00
> > > There were 90 inconsistent shifts. Check your topology
> > > Large VCM(group rest):      0.00420,     -0.00470,     -0.00106,
> > > ekin-cm:  1.82364e+00
> > > 
> > > There is anyone that with that information have any idea of what is
> > > going on. I'm sorry but I can't understand this message. Check what of
> > > the topology file. My topology file was made by PRODRG and extended by
> > > me manually, The system are 255 monomers of 
> > > 8C's-benzene-N=N-benzene-O-3C's-COOH monom in vacum. If you need
> > > anything else just tell me. 
> > > 
> > > Thanks in advance.
> > > 
> > > Hector Martínez-Seara Monné 
> > > 
> > > Universidad Barcelona 
> > > Dpt. Química-Física 
> > >  
> > > 
> > > 
> > > 
> > > ______________________________________________________________________
> > > _______________________________________________
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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