[gmx-users] MD of polymer in pbc
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 26 12:23:08 CET 2002
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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