[gmx-users] NPT for compressing
Elisabeth
katesedate at gmail.com
Sun May 22 03:58:40 CEST 2011
On 20 May 2011 23:04, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.
>
> Hello Mark,
>
> My box of alkane was already equilibrated using a NVT run. I just have to
> increase the density.
> After NVT run, do I have to turn off gen_vel = yes for NPT
> run? Is this necessary for all NPT runs?
>
> 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?
>
> I meant
>
; Bonds
> constraints = none
>
not restraining position of atoms.
Thanks,
> 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.
>
>
> We can't tell.
>
> Mark
>
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