[gmx-users] rotate in editconf

[Attilio Vargiu]

Hi Tsjerk,
first, thanks for the answer!
I already tried to generate a new box, rotating also the "box vectors" at the
end of the gro file.
But I read in the manual online that the gro format only supports cubic box in
which the box vectors coincide with the axis, so I dont know how to do! In
addition I tried to find something about g96 format, without success...
 

Scrive "T.A.Wassenaar" <T.A.Wassenaar at rug.nl>:

> 
> 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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