Dear experts,<br><br>I have a box of pure hexane with density of around 50 SI (size 7nm). With the settings below I get error: <br><br>vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05 2011<br>Warning: 1-4 interaction between 1246 and 1249 at distance 3.580 which is larger than the 1-4 table size 2.250 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br>Warning: 1-4 interaction between 1249 and 1252 at distance 3.693 which is larger than the 1-4 table size 2.250 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br><br>A list of missing interactions:<br>
Bond of 2375 missing 2<br> Angle of 4500 missing 11<br> Ryckaert-Bell. of 5625 missing 21<br> LJ-14 of 5625 missing 15<br><br>Molecule type 'Hexane'<br>
the first 10 missing interactions, except for exclusions:<br> Ryckaert-Bell. atoms 5 8 11 14 global 1245 1248 1251 1254<br> LJ-14 atoms 5 14 global 1245 1254<br> Angle atoms 8 11 14 global 1248 1251 1254<br>
Ryckaert-Bell. atoms 8 11 14 15 global 1248 1251 1254 1255<br> Ryckaert-Bell. atoms 8 11 14 16 global 1248 1251 1254 1256<br> Ryckaert-Bell. atoms 8 11 14 17 global 1248 1251 1254 1257<br>
LJ-14 atoms 8 15 global 1248 1255<br> LJ-14 atoms 8 16 global 1248 1256<br> Ryckaert-Bell. atoms 9 8 11 14 global 1249 1248 1251 1254<br> LJ-14 atoms 9 14 global 1249 1254<br>
<br>-------------------------------------------------------<br>Program mdrun_mpi, VERSION 4.5.4<br>Source code file: domdec_top.c, line: 356<br><br>Fatal error:<br>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<br>
For more information and tips for troubleshooting, please check the GROMACS<br>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br><br><br><br>mdp file:<br><br>
; Bonds<br>
constraints = none <br>
constraint-algorithm = lincs <br><br>; Run control <br>integrator = md <br>dt = 0.001 <br>nsteps = 500000 ;5000 <br>
nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>
nstxout = 100;1 <br>nstvout = 0<br>nstfout = 0<br>nstlog = 1000 ; frequency to write energies to log file<br>nstxtcout = 1000 <br>
<br>; Neighbor searching<br>nstlist = 10 <br>ns_type = grid <br><br>; Electrostatics/VdW <br>coulombtype = Shift <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0.9 ;0 <br><br>; Cut-offs<br>rlist = 1.25 <br>rcoulomb = 1.0 <br>rvdw = 1.0 <br>
<br>; Temperature coupling <br>Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 <br>ref_t = 300 <br><br>; Pressure coupling<br>
Pcoupl = Parrinello-Rahman <br>Pcoupltype = isotropic <br>tau_p = 1 <br>compressibility = 4.5e-5 4.5e-5 <br>ref_p = 10 <br>
<br>; Velocity generation <br>gen_vel = yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br> <br>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.<br>
<br>
<p class="MsoNormal"><span style="">10 bar</span></p>
<p class="MsoNormal" style=""><span style="font-family: "Courier New";">;<span style=""> </span>Pressure
coupling</span></p>
<p class="MsoNormal" style=""><span style="font-family: "Courier New";">Pcoupl<span style=""> </span>=<span style="">
</span>berendsen</span></p>
<p class="MsoNormal" style=""><span style="font-family: "Courier New";">Pcoupltype<span style=""> </span><span style=""> </span>=<span style="">
</span>isotropic<span style=""> </span><span style=""> </span></span></p>
<p class="MsoNormal" style=""><span style="font-family: "Courier New";">tau_p<span style=""> </span>= <b style=""><span style=""> </span>0.1 </b><span style=""> </span>0.5<span style=""> </span><span style=""> </span><span style=""> </span></span></p>
<p class="MsoNormal" style=""><span style="font-family: "Courier New";">compressibility<span style=""> </span>=<span style="">
</span>4.5e-5 4.5e-5<span style=""> </span> </span></p>
<p class="MsoNormal"><span style="font-family: "Courier New";">ref_p<span style=""> </span>=<span style=""> </span>10<span style=""> </span>10<span style=""> </span></span><span style=""></span></p>
<p class="MsoNormal"><span style=""> </span></p>
<p class="MsoNormal"><span style="">does not compress!
With and without constr.</span></p>
<br><br><br>Best,<br>