[gmx-users] rotate in editconf

[Attilio]

Hi all,

I'm trying to implement umbrella sampling on my system.
My reaction coordinate is a distance between two atoms A and B.
Before starting the dynamics I rotated the system in order to align the 
vector AB with the z axis. To rototranslate the system I used editconf 
with the flag -rotate.
In this manner I apply an harmonic constraint only in the z direction, 
allowing the system to explore phase space in the xy plane. This is my 
pull.ppa file:

verbose = yes
runtype=umbrella
group_1=C_IMI
reference_group=N_GUA
reftype=com
weights_1=
pulldim=N N Y
k1=15000;kJ/mol-1/nm-2
pos1= 0 0 0.422

But the dynamics died after 1-2 min, with this error:

There are 24895 atoms in your xtc output selection

t = 0.000 ps: Water molecule starting at atom 12323 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Large VCM(group IMI):     -0.05608,     -0.16218,     -0.08893, 
ekin-cm:  5.55321e+00
Group IMI with mass  2.97308e+02, Ekrot  6.00893e+00 Det(I) =  1.31027e+02
  COM:      4.21794       4.56359       3.70009
  P:      -16.67273     -48.21760     -26.44075
  V:       -0.05608      -0.16218      -0.08893
  J:       11.75914     -12.46278      17.04114
  w:        0.39515      -0.24657       0.25223
Inertia tensor (3x3):
   Inertia tensor[    0]={ 3.36886e+01, -1.93692e+00, -1.95062e+01}
   Inertia tensor[    1]={-1.93692e+00,  9.88940e-01,  2.37864e+00}
   Inertia tensor[    2]={-1.95062e+01,  2.37864e+00,  1.75272e+01}
Long Range LJ corr. to Epot:   -891.161, Pres:   -118.079, Vir:    5346.96
   Energies (kJ/mol)
           Bond       G96Angle    Proper Dih.          LJ-14     Coulomb-14
    8.73471e+02    1.88436e+03    2.22140e+03    8.62560e+02   -1.32192e+04
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR) Position Rest.
    4.79055e+17   -8.91161e+02   -3.15962e+05   -2.24687e+04    0.00000e+00
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
    4.79055e+17            nan            nan            nan            nan


t = 0.000 ps: Water molecule starting at atom 12446 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.000 ps: Water molecule starting at atom 12446 can not be settled.
..........
..........
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates

t = 0.001 ps: Water molecule starting at atom 12446 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Grid: -2147483648 x -2147483648 x -2147483648 cells
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]

Then I tried to run the original (without rototranslation) system, and 
this works without problems (I tried both a normal dynamics and the one 
with the umbrella code).
Incidentally I visualized with VMD both the system, and it seems that 
periodic conditions are not well conserved in the rototranslated system. 
In fact a simulation of this latter without periodic conditions proceed 
well.

Does anybody kwow how to deal with this problem?
Many thanks in advance,

Attilio

-- 
Attilio Vittorio Vargiu
PhD Student at SISSA/ISAS
via Beirut 4
I-34014 Trieste, Italy
tel +390403787335   fax +390403787528