[gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul <jalemkul at vt.edu> 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.
>> -------------------------------------------------------
>>
>> I tried all vdwtype options to see whether this would mitigate the issues
>> but was unsuccessful.
>> 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.
>>
>>
> It seems to me that your system is simply too small to perform this kind of
> operation.  By applying 1000 bar of pressure to such a small system, you can
> certainly expect the box size to deform and get smaller.  Perhaps a larger
> number of molecules (and thus a larger box) will give you a reasonably-sized
> box once the 1000 bar of pressure has been applied and the system
> equilibrated.
>

Yes I think I should increase my simulation size as pointed out by Mark.


> Also note that haphazardly changing the vdwtype or rvdw can have negative
> impacts on your simulation, depending on your chosen force field's
> sensitivity to these parameters.
>

Thank you for pointing this out. I am relatively new to this method so am
taking "figure out as I go" approach.


-Justin
>
>  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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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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