[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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