[gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I am running an NPT simulation with 100 molecules of n-alkane and trying
>> to impose uni-axial pressure of these molecules using semiisotropic option
>> in grompp.mdp.
>> However, as the box seems to distort significantly due to the imposed
>> pressure which leads to the following error message:
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0.5
>> Source code file: ns.c, line: 2295
>>
>> Fatal error:
>> One of the box vectors has become shorter than twice the cut-off length or
>> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>> -------------------------------------------------------
>>
>
> You're imposing 1000 bar of pressure along the z-axis. Surely you should
> expect distortion?
>
> You should do some maths and work out the expected density of the box under
> such pressure. You still need a box large enough that the maximum cut-off
> length can be satisfied, so that sets the minimum number of molecules you
> need, and thus the initial size of the box.
>
>
Thanks for the input. I should do this.




>
>  I tried all vdwtype options to see whether this would mitigate the issues
>> but was unsuccessful.
>>
>
> Don't fool with .mdp settings hoping it'll magically work. Read how they
> work, and you might have understood why the minimum image convention
> requires that the condition that provoked the above error does not arise.
>
> Mark
>
 is there any other options in gromacs that I can use to impose uniaxial
>> stress? Or does anyone had any similar problems related to semi-isotropic
>> pressure coupling?
>> Thank you in advance.
>>
>> This is my grompp.mdp file configuration:
>> integrator          =  md
>> dt                  =  0.001 ; ps !
>> nsteps              =  1000000 ; nstcomm             =  1
>> nstxout             =  250 ; collect data every 0.5 ps
>> nstvout             =  1000
>> nstfout             =  0
>> nstlog              =  10
>> nstenergy           =  10
>> nstlist             =  10
>> ns_type             =  grid
>> rlist               =  0.9
>>
>> coulombtype            =  PME
>> rcoulomb            =  0.9
>> vdwtype             =  switch
>> rvdw                =  0.7
>> rvdw_switch         =  0.0
>>
>> fourierspacing  =  0.12
>> fourier_nx  =  0
>> fourier_ny  =  0
>> fourier_nz  =  0
>> pme_order  =  4
>> ewald_rtol  =  1e-5
>> optimize_fft  =  yes
>> ; temperature coupling is on
>> Tcoupl                      =  v-rescale
>> ; Groups to couple separately
>> tc-grps                  = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t                    = 0.1
>> ref_t                    = 300
>> ; Generate velocites is on at 300 K.
>> gen_vel             =  yes
>> gen_temp            =  300.0
>> gen_seed            =  173529
>> constraints              = all-bonds
>>
>> ; pressure coupling is on
>> pcoupl = parrinello-rahman
>> pcoupltype = semiisotropic
>>
>> tau_p = 0.5
>> compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
>> ref_p = 1.0 1000.0                  ;x/y-direction, z-direction
>>
>>
>>
>> --
>> Yongchul "Greg" Chung
>> Graduate Student
>> Dept. of Chemical Engineering, Case Western Reserve University
>>
>>
>> ------------------------------------------------------------------------
>>
>>
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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