[gmx-users] NPT for compressing

[Elisabeth]

Dear  experts,

I have a box of pure hexane with density of around 50 SI (size 7nm). With
the settings below I get error:

vol 0.65  imb F  3% step 42100, will finish Fri May 20 18:54:05 2011
Warning: 1-4 interaction between 1246 and 1249 at distance 3.580 which is
larger than the 1-4 table size 2.250 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Warning: 1-4 interaction between 1249 and 1252 at distance 3.693 which is
larger than the 1-4 table size 2.250 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

A list of missing interactions:
                Bond of   2375 missing      2
               Angle of   4500 missing     11
      Ryckaert-Bell. of   5625 missing     21
               LJ-14 of   5625 missing     15

Molecule type 'Hexane'
the first 10 missing interactions, except for exclusions:
      Ryckaert-Bell. atoms    5    8   11   14 global  1245  1248  1251
1254
               LJ-14 atoms    5   14           global  1245  1254
               Angle atoms    8   11   14      global  1248  1251  1254
      Ryckaert-Bell. atoms    8   11   14   15 global  1248  1251  1254
1255
      Ryckaert-Bell. atoms    8   11   14   16 global  1248  1251  1254
1256
      Ryckaert-Bell. atoms    8   11   14   17 global  1248  1251  1254
1257
               LJ-14 atoms    8   15           global  1248  1255
               LJ-14 atoms    8   16           global  1248  1256
      Ryckaert-Bell. atoms    9    8   11   14 global  1249  1248  1251
1254
               LJ-14 atoms    9   14           global  1249  1254

-------------------------------------------------------
Program mdrun_mpi, VERSION 4.5.4
Source code file: domdec_top.c, line: 356

Fatal error:
49 of the 18125 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off distance
(1.25 nm) or the two-body cut-off distance (1.25 nm), see option -rdd, for
pairs and tabulated bonds also see option -ddcheck
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



mdp file:

;        Bonds
constraints             = none
constraint-algorithm = lincs

;        Run control
integrator          =  md
dt                  =  0.001
nsteps              =  500000 ;5000
nstcomm             =  100

;        Output control
nstenergy           =  100                  ; frequency to write energies to
energy file. i.e., energies and other statistical data are stored every 10
steps
nstxout             =  100;1
nstvout             =  0
nstfout             =  0
nstlog              =  1000                 ; frequency to write energies to
log file
nstxtcout          =  1000

;        Neighbor searching
nstlist             =  10
ns_type             =  grid

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

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

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

;        Pressure coupling
Pcoupl              =  Parrinello-Rahman
Pcoupltype          =  isotropic
tau_p               =  1
compressibility     =  4.5e-5 4.5e-5
ref_p               =  10

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


When I use constraints for all-bonds and dt of 0.002 compressing the box
works well and I get density of above 600 SI which is the actual density of
alkane. Can any one help why setting no constraints and dt=0.001 leads to
the error message shown above. When no constraints is used PR doesnt work
for compressing and berendsen gives desired densty only for high pressures
above 50 bar. I need to study my system at different pressures from 10
bar... please comment on this.. Thanks.

10 bar

;           Pressure coupling

Pcoupl              =  berendsen

Pcoupltype          =  isotropic

tau_p               = * 0.1 *   0.5

compressibility     =  4.5e-5 4.5e-5

ref_p               =  10     10



does not compress! With and without constr.



Best,
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