# [gmx-users] rhdo box shape changed during simulation

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 2 21:27:28 CET 2006

```Hi Liang,

I'm not completely sure on this one, but isn't parinello-rahman per
definition anisotropic? Check the manual.
Regarding the second question, my usual answer is "there's no such
thing as a box in the infinite simulation system". There's only the
lattice, which is defined by three vectors. But whether the shape of
the unit cell is allowed to change depends on the pressure coupling
you use. When using isotropic pressure coupling you're using a scalar
to scale the box vectors and your box shape (the angles between your
vectors and the relative lengths) will be retained. But if I recall
correctly, parinello-rahman works by changing the box vectors based on
the "velocities" of these box vectors, which are scaled at every step
to relax to the desired pressure. Thus, anisotropic pressure scaling.
You could try to use Berendsen pressure coupling.

Best,

Tsjerk

On 11/2/06, Liang Ma <liang.ma.1983 at gmail.com> wrote:
> Hi Tsjerk,
>     Thanks for you fast reply. :-):-) Yes, I indeed used the isotropic
> pressure scaling method.  That's why I found it's surpring that one
> dimension of my system actually shrinked. Is there any other possible reason
> for this? Or, is there any constraint to keep the box shape always
> rhdo-like?  If not, does gromacs always treat rhdo as triclinic and the box
> shaple actually is free to change?
>
>
> Thanks a lot!
>
> Liang
>
> This is my grompp file:
>
> ; title and include files
> title                    = salt
> cpp                      = cpp
> include                  =
> -I/home/ma/gromacs/share/gromacs/top -I./
> define                   =
> ; integrator and input/output setting up
> integrator               = md
> nsteps                   = 600000 ; 1.2 ns equilibration
> dt                       = 0.002
> nstxout                  = 5000
> nstvout                  = 5000
> nstenergy                = 500
> nstxtcout                = 500
> nstlog                   = 500
> xtc_grps                 = System
> energygrps               = System
> comm_mode                = none
> ; neighbor searching and vdw/pme setting up
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.4
>
> coulombtype              = pme
> fourierspacing           = 0.1
> pme_order                = 6
> rcoulomb                 = 1.4
>
> vdwtype                  = switch
> rvdw_switch              = 1.0
> rvdw                     = 1.2
>
> ; cpt control
> tcoupl                   = nose-hoover
> tc-grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300
> Pcoupl                   = parrinello-rahman
> pcoupltype               = isotropic
> tau_p                    = 1.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
>
> ; velocity & temperature control
> gen_vel                  = no
> gen_temp                 = 300
> annealing                = no
> constraints              = hbonds
> constraint_algorithm     = shake
> morse                    = no
>
>
>
>
> On 11/2/06, Tsjerk Wassenaar < tsjerkw at gmail.com> wrote:
> >
> > Hi Liang,
> >
> > Apparently, your system contracted in one direction. You can avoid
> > this by simulating at constant volume or by using isotropic pressure
> > coupling.
> > Your protein should not have direct interactions with its periodic
> > images during the simulation. This usually means you can discard your
> > results.
> > The last two values are the x and y skewing of the third vector
> > defining your periodic lattice (the periodic boundary conditions).
> > Likewise, the first two zeros are the y and z skewing of the first
> > vector and the other two zeros are the x and z skewing of the second
> > vector. You can check chapter 3 of the gromacs manual to get to know
> > more about periodic boundary conditions in gromacs.
> >
> > Best,
> >
> > Tsjerk
> >
> > On 11/2/06, Liang Ma <liang.ma.1983 at gmail.com> wrote:
> > > Hi all gromacs users,
> > >      I am simulating a protein in explicit solvent with Periodic
> boundary
> > > condition and PME . The box type I used
> > > is rhdo (rhombic dodecahedron). However, I checked the box length and
> angle
> > > during simulations,  it  deviates far away from the normal rhdo box
> shape.
> > > For example, the third line  in  pdb  at the beginning is :
> > >  CRYST1   90.093   90.093   90.093  60.00  60.00  90.00 P 1           1
> > > which is a perfect rhdo box.
> > >
> > > During the simulation, it changed to:
> > > CRYST1   89.503   89.503   68.425 105.59 105.59  90.00 P 1           1
> > > ,which is not rhdo.
> > > Meanwhile, the distance between the protein and its nearst image
> decreased
> > > dramatically, (they even touched).
> > > So my question is this normal? If not, is there any way to constraint
> the
> > > box always in a rhdo box shape (a=b=c)
> > >
> > > And also,
> > > the last line in the gro file changed to:
> > > 8.95030   8.95030   6.32914   0.00000   0.00000   0.00000   0.00000
> > > -1.83879  -1.83879
> > > what does the last two negative values exactly mean?
> > >
> > >
> > >  Thanks for any help!
> > > Liang
> > >
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> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > post-doc
> > NMR, Utrecht University,
> > 3584 CH Utrecht, the Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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--
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,