[gmx-users] semiisotropic pressure coupling

[Justin A. Lemkul]

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.

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.

-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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