[gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

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.

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091025/da2bb9cb/attachment.html>