[gmx-users] rhdo box shape changed during simulation
Liang Ma
liang.ma.1983 at gmail.com
Thu Nov 2 21:57:17 CET 2006
Hi Tsjerk,
Thanks for the hint. :-) I will check the compatability of isotropic
scaling and parinello-rahman method. Thanks!
Liang
On 11/2/06, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> 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,
> > > Padualaan 8,
> > > 3584 CH Utrecht, the Netherlands
> > > P: +31-30-2539931
> > > F: +31-30-2537623
> > > _______________________________________________
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> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> post-doc
> NMR, Utrecht University,
> Padualaan 8,
> 3584 CH Utrecht, the Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
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