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.
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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