[gmx-users] rhdo box shape changed during simulation

[Liang Ma]

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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