[gmx-users] NPT for compressing

[Mark Abraham]

On 21/05/2011 10:45 AM, Elisabeth wrote:
> 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

OK, your system blew up.

>
> 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

Generating velocities and compressing from an unequilibrated initial 
conformation in the same run is asking for trouble, and sometimes you're 
observing it. See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. 
Equilibrate first. Then slowly change the conditions so that you're 
never all that far from equilibrium, and reach your destination.

> 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. 

You probably got lucky the first time and not the second. Or, your 
atom-atom bond interactions are no good.

> When no constraints is used PR doesnt work for compressing

So you want to restrain the positions of heavy atoms, but compress a 
pure system? This is contradictory. How do you want to decrease the 
volume if the atoms aren't allowed to move much?

> 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=1010
>
> does not compress! With and without constr.
>

We can't tell.

Mark
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