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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