[gmx-users] MD of polymer in pbc

Ester Chiessi ester.chiessi at uniroma2.it
Tue Nov 26 12:52:21 CET 2002


Thanks David for your answer.

In every calculation I already used:

setenv GMXFULLPBC 1.

Ester




David van der Spoel wrote:

> On Tue, 2002-11-26 at 12:14, Ester Chiessi wrote:
> > Hi Gromacs people,
> >
> > I'm working to perform molecular dynamics simulations of a polymer in PBC and I
> > found some problems.
> >
> > After preliminary minimizations and preparations of the system (with no problem if
> > I don't insert the connectivity accross boundaries), I received this message during
> > the minimization of the 'infinite' chain:
> > ...........
> > Removing pbc first time.
> > There were 2 inconsistent shifts. Check your topology.
> > Done rmpbc.
>
> try setting
> setenv GMXFULLPBC 1
>
> if you have an inifinite molecule (i.e. circular)
>
> > ...........
> > I tried the following dynamics that couldn't start.
> >
> > This is part of the output file md0.log :
> >
> > There are: 355 Atom
> > Removing pbc first time
> > There were 2 inconsistent shifts. Check your topology
> > Done rmpbc
> >
> > Constraining the starting coordinates (step -2)
> >
> > ............
> >
> > Initializing LINear Constraint Solver
> >   number of constraints is 40
> >   average number of constraints coupled to one constraint is 2.5
> >
> >    Rel. Constraint Deviation:  Max    between atoms     RMS
> >        Before LINCS         14.051325     37     38   2.221738
> >         After LINCS         7.971895     38     39   1.863314
> >
> >
> > Step -2, time -0.004 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 7.971895 (between atoms 38 and 39) rms 1.863314
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >       1      2   88.9    0.1527   0.4141      0.1530
> >      38      1   97.4    0.1510   1.0500      0.1530
> >      33     34   90.8    0.1521   0.4259      0.1530
> >      34     35   91.2    0.1444   0.4658      0.1430
> >      34     37   99.2    0.1515   0.8675      0.1530
> >      37     38   94.4    2.3029   0.5622      0.1530
> >      38     39   88.1    0.1450   1.2830      0.1430
> >      39     40   52.1    0.1018   0.1484      0.1000
> > Constraint error in algorithm Lincs at step -2
> >
> > Constraining the coordinates at t0-dt (step -1)
> >    Rel. Constraint Deviation:  Max    between atoms     RMS
> >        Before LINCS         7.959223     38     39   1.862687
> >         After LINCS         5.711798     37     38   1.211940
> >
> >
> > Step -1, time -0.002 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 5.711798 (between atoms 37 and 38) rms 1.211940
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >       1      2  105.5    0.4141   0.2115      0.1530
> >      38      1   96.1    1.0500   0.0735      0.1530
> >       2      3   66.3    0.1245   0.1508      0.1430
> >       3      4   44.3    0.1007   0.1377      0.1000
> >       5      6   39.0    0.1533   0.1779      0.1530
> >      33     34  100.5    0.4259   0.3628      0.1530
> >      34     35   90.3    0.4658   0.5381      0.1430
> >      34     37   99.1    0.8675   0.4135      0.1530
> >      35     36   88.1    0.0396   0.2269      0.1000
> >      37     38   98.9    0.5622   1.0269      0.1530
> >      38     39   82.5    1.2830   0.1497      0.1430
> >      39     40   85.2    0.1484   0.4389      0.1000
> > Constraint error in algorithm Lincs at step -1
> >
> > Started mdrun on node 0 Mon Nov 25 13:06:01 2002
> > Initial temperature: 257962 K
> > Grid: 4 x 4 x 4 cells
> > Using buffers of length 1000 for innerloop vectorization.
> > Full PBC calculation = TRUE
> >            Step           Time         Lambda      Annealing
> >               0        0.00000        0.00000        1.00000
> >
> >    Rel. Constraint Deviation:  Max    between atoms     RMS
> >        Before LINCS         16.617081     34     37   4.842547
> >         After LINCS         7.988674     27     28   2.490661
> >
> >
> > Step 0, time 0 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 7.988674 (between atoms 27 and 28) rms 2.490661
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >       1      2   96.0    0.4141   0.8453      0.1530
> >      38      1   91.9    1.0500   0.9421      0.1530
> >       2      3   59.2    0.1245   0.1394      0.1430
> >       3      4   38.5    0.1007   0.1243      0.1000
> >      25     26   90.1    0.1532   0.3909      0.1530
> >      26     27   90.0    0.1432   0.8420      0.1430
> >      26     29   90.7    0.1534   0.3886      0.1530
> >      27     28   90.0    0.1000   0.8989      0.1000
> >      33     34   97.3    0.4259   0.7285      0.1530
> >      34     35   87.9    0.4658   0.8409      0.1430
> >      34     37   90.2    0.8675   0.9391      0.1530
> >      37     38  107.8    0.5622   0.3559      0.1530
> >      38     39   83.6    1.2220   0.4566      0.1430
> >      39     40   89.8    0.1484   0.7116      0.1000
> > Constraint error in algorithm Lincs at step 0
> >
> > t = 0.000 ps: Water molecule starting at atom 74 can not be settled.
> > Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and
> > current coordin
> > ates
> >    Energies (kJ/mol)
> >           Angle    Proper Dih.          LJ-14     Coulomb-14        LJ (SR)
> >     2.52067e+03    7.33230e+01    2.90584e+01   -6.53393e+02    1.34327e+05
> >    Coulomb (SR)      Potential    Kinetic En.   Total Energy    Temperature
> >    -2.18829e+04    1.14414e+05           NaNQ           NaNQ           NaNQ
> >  Pressure (bar)
> >            NaNQ
> >
> >            Step           Time         Lambda      Annealing
> >               5        0.01000        0.00000        1.00000
> >
> > xx[    0] before: (    NaNQ,    NaNQ,    NaNQ) After: (    NaNQ,    NaNQ,    NaNQ)
> > xx[    1] before: (    NaNQ,    NaNQ,    NaNQ) After: (    NaNQ,    NaNQ,    NaNQ)
> >  ..............
> > Atoms 33-40 are at the end of the chain. 38 is periodically linked to 1.
> >
> > I'm quite sure the topology is OK.
> > (The same dynamics calculation on the chain 'not infinite' don't give problem).
> >
> > Thanks for any suggestion.
> >
> > Ester
> >
> >
> > --
> > Ester Chiessi
> > Dipartimento di Scienze e Tecnologie Chimiche
> > Universita' di Roma "Tor Vergata"
> > Via della Ricerca Scientifica
> > 00133 Roma (Italy)
> > http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
> > e-mail: ester.chiessi at uniroma2.it
> > Phone: 39*6*72594462
> >        39*6*72594874
> > Fax:39*6*72594328
> >
> >
> > _______________________________________________
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> >
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,          75123 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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--
Ester Chiessi
Dipartimento di Scienze e Tecnologie Chimiche
Universita' di Roma "Tor Vergata"
Via della Ricerca Scientifica
00133 Roma (Italy)
http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm
e-mail: ester.chiessi at uniroma2.it
Phone: 39*6*72594462
       39*6*72594874
Fax:39*6*72594328





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