[gmx-users] MD of polymer in pbc

[Ester Chiessi]

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.
...........
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