[gmx-users] number of DD cells

[Moeed]

Hello,

I am attempting to increase the density using NPT. As I increase the
pressure to compress the system after some steps simulation crashes. I
thought maybe its becasue I am compressing too fast but even when I take a
stepwise approach to compress gradually the same error comes up. The density
at the point of crash is about 30 SI while I need 650 which is the actual
density. Topology file is generated successfully and also I did EM before
MD.

Initial box size is 30 nm. As suggested in the link below I reduced the size
to 20 nm (there are 2500 atoms in the system ) but the same error appears.
http://lists.gromacs.org/pipermail/gmx-users/2009-April/041488.html

I also tried less -np from 7 to 4 but no success.

Can you please tell me what this exclamation mark mean which I get at times
in parallel trials.(vol 0.99 !)

Thank you for your time.


vol 0.99! imb F 47% step 168000, will finish Fri Mar  4 00:51:29 2011
vol 0.99! imb F 42% step 168100, will finish Fri Mar  4 00:51:26 2011
vol 0.99! imb F 44% step 168200, will finish Fri Mar  4 00:51:30 2011
vol 1.00! imb F 46% step 168300, will finish Fri Mar  4 00:51:27 2011
vol 1.00! imb F 48% step 168400, will finish Fri Mar  4 00:51:25 2011

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 2592

Fatal error:
The X-size of the box (5.499734) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (7) times the smallest allowed cell
size (0.785678)
========================================

Program mdrun_mpi, VERSION 4.0.7
Source code file: domdec.c, line: 2592

Fatal error:
The X-size of the box (4.999741) times the triclinic skew factor (1.000000)
is smaller than the number of DD cells (4) times the smallest allowed cell
size (1.250000)

====================================
pbc              =  xyz


;        Run control
integrator          =  md
dt                  =  0.002
nsteps              =  1000000 ;5000
nstcomm             =  100

;        Output control
nstenergy           =  100
nstxout             =  100
nstvout             =  0
nstfout             =  0
nstlog              =  1000
nstxtcout          =  1000

;        Neighbor searching
nstlist             =  10
ns_type             =  grid

;        Electrostatics/VdW
coulombtype         =  PME
vdw-type            =  Shift
rcoulomb-switch     =  0
rvdw-switch         =  0.9 ;0

;        Cut-offs
rlist               =  1.25
rcoulomb            =  1.25 ;1.1
rvdw                =  1.0

;        PME parameters
fourierspacing      =  0.3
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order          =  4
ewald_rtol         =  1e-5
optimize_fft      =  yes

;        Temperature coupling
Tcoupl              =  v-rescale
tc-grps             =  System  ;HEX
tau_t               =  0.1     ;0.1
ref_t               =  400     ;300

;        Pressure coupling
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  1      1           ;0.5
compressibility     =  4.5e-5 4.5e-5
ref_p               =  8    8

;        Velocity generation
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

;        Bonds
constraints             = all-bonds
constraint-algorithm = lincs
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