[gmx-users] rotate in editconf

[T.A.Wassenaar]

Hi Attilio,

Do you construct a new box after rotation? editconf does 
not change the box when rotating a system, and besides, 
the box would probably be invalid anyway. So if you 
haven't done so, try to generate a new box for the rotated 
system (translation doesn't matter).

Hope it helps,

Tsjerk


On Wed, 06 Jul 2005 17:21:08 +0200
  Attilio <vargiu at sissa.it> wrote:
> 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
> 
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