[gmx-users] Exploding box (in one dimension) Semi-isotropic pressure coupling?

[sapna sarupria]

Hi Sander
Thanks for your response. Is there then a preference for z-dimension to
expand (other than the way the system is setup in terms of semi-isotropic
coupling). Would one see an expansion in any one direction if I had the same
system setup with independent pressure coupling for each dimension
(anisotropic)?

Thanks,
Sapna

On Tue, Mar 30, 2010 at 11:53 AM, Sander Pronk <pronk at cbr.su.se> wrote:

> It sounds like the normal thing that would happen if you have a system that
> has no shear elastic constant, like a fluid.
> In that case, there are no restoring forces against growth of system size
> in one coordinate with a concomitant decrease in the other coordinates, so
> eventually this should happen (unless I misunderstand the nature of your
> system).
>
> Sander
>
>
> On Mar 30, 2010, at 17:47 , sapna sarupria wrote:
>
> Hello all,
>
> I have a simulation running for a hydrate (with CO2) and water in contact
> with each other. I run the simulation at 280K at which the hydrate melts and
> finally the system is just liquid water with CO2 in it. However, as the
> simulation proceeds the box begins to expand in the z-direction and
> decreases in the x-y direction considerably. Initially the box has
> 4.8x4.8x9.6 nm^3 dimensions. After the hydrate melts (the volume fluctuates
> more) and is fine for another 10 ns but after that the dimensions in the x-y
> direction decrease to 2.5 nm and z-dimension increases to 35 nm. At this
> point the simulation crashes since my cut-off distance are 1.2 nm.
>
> I am using semi-isotropic pressure coupling but the pressure in the x-y
> direction and z-direction are the same (=30.5 bar) and so is the
> compressibility (=4.5e-5). I am using Parrinello-Rahman pressure coupling
> and Nose-Hoover thermostat. The CO2 and water molecules are rigid and shake
> is used to maintain their geometry. The simulation time step is 2 fs. Can
> someone tell me why such a thing happens? I have pasted my mdp file for
> completeness. I am using Gromacs  4.0.5 and I run the simulations in
> parallel using 4 processors. Values related to domain decomposition etc are
> unchanged and the default values are used.
>
> Any insights will be helpful. Thanks for the help.
>
> MDP File:
> title               =  CO2 hydrate + water      ; a string
> cpp                 =  /lib/cpp                 ; c-preprocessor
> dt                  =  0.002                    ; time step
> nsteps           =  25000000            ; number of steps
> nstcomm       =  10                           ; reset c.o.m. motion
> nstxout          =  20000                    ; write coords
> nstvout          =  20000                    ; write velocities
> nstlog            =  25000                    ; print to logfile
> nstenergy      =  500                   ; print energies
> xtc_grps        =  OW_HW1_HW2_CO2
> nstxtcout       =  500
> nstlist             =  10                       ; update pairlist
> ns_type          =  grid                     ; pairlist method
> coulombtype   =  PME
> rvdw                =  1.2                      ; cut-off for vdw
> rcoulomb         =  1.2                      ; cut-off for coulomb
> rlist                  =  1.2                      ; cut-off for coulomb
> DispCorr          =  EnerPres
> Tcoupl              =  Nose-Hoover
> ref_t                 =  300
> tc-grps             =  System
> tau_t                 =  0.5
> Pcoupl              =  Parrinello-Rahman
> Pcoupltype       =  semiisotropic            ; pressure geometry
> tau_p               =  1.0   1.0                ; p-coupling time
> compressibility     =  4.5e-5  4.5e-5           ; compressibility
> ref_p               =  30.5  30.5               ; ref pressure
> gen_vel             =  yes                      ; generate initial vel
> gen_temp            =  200                      ; initial temperature
> gen_seed            =  372340                   ; random seed
> constraint_algorithm = shake
> constraints         =  all-bonds
>
>
>
> Thanks a lot
>  Sapna
>
>
>
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