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

[sapna sarupria]

Hi Sander

That helps quite a bit. Thanks so much!

Sapna

On Tue, Mar 30, 2010 at 12:50 PM, Sander Pronk <pronk at cbr.su.se> wrote:

> There *should* be no preference, but I seem to remember that one of the
> artifacts of using Ewald-style electrostatic treatment (such as PME) is that
> there may be dipole-coupling between periodic images, especially if one
> symmetry has already been broken.
> That doesn't mean you shouldn't use PME, though: you're a long way off from
> the thermodynamic limit, so you can't rely on fluctuations being slow. The
> situation you're describing will always happen, and with a small number of
> particles (i.e. less than you can see with the naked eye) it will happen
> sooner rather than later.
>
> Sander
>
>
> On Mar 30, 2010, at 18:00 , sapna sarupria wrote:
>
> 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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