I obtain the following output:
*Steepest Descents:*
* Tolerance (Fmax) = 1.00000e+03*
* Number of steps = 1000*
*Step= 0, Dmax= 1.0e-02 nm, Epot= 1.21621e+06 Fmax= 2.24275e+08,
atom= 12592*
*Step= 1, Dmax= 1.0e-02 nm, Epot= -4.92685e+05 Fmax= 1.05309e+07,
atom= 12585*
*Step= 2, Dmax= 1.2e-02 nm, Epot= -6.65927e+05 Fmax= 2.33570e+06,
atom= 12586*
*Step= 3, Dmax= 1.4e-02 nm, Epot= -7.19859e+05 Fmax= 2.16295e+06,
atom= 12585*
*Step= 4, Dmax= 1.7e-02 nm, Epot= -7.53908e+05 Fmax= 8.32452e+05,
atom= 12586*
*Step= 5, Dmax= 2.1e-02 nm, Epot= -7.75691e+05 Fmax= 9.90803e+05,
atom= 12585*
*Step= 6, Dmax= 2.5e-02 nm, Epot= -7.98119e+05 Fmax= 9.99586e+04,
atom= 12730*
*Step= 7, Dmax= 3.0e-02 nm, Epot= -8.47120e+05 Fmax= 7.37766e+05,
atom= 12585*
*
*
*Step 8, time 0.008 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 0.000009, max 0.000105 (between atoms 12731 and 12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12586 12585 32.1 0.0936 0.0936 0.0936*
*Step= 8, Dmax= 3.6e-02 nm, Epot= -8.55218e+05 Fmax= 5.79704e+04,
atom= 12585*
*Step= 9, Dmax= 4.3e-02 nm, Epot= -8.92739e+05 Fmax= 1.11595e+05,
atom= 12585*
*
*
*Step 10, time 0.01 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 0.000045, max 0.000529 (between atoms 12731 and 12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12586 12585 46.3 0.0934 0.0936 0.0936*
* 12731 12730 31.3 0.0936 0.0936 0.0936*
*Step= 10, Dmax= 5.2e-02 nm, Epot= -9.06732e+05 Fmax= 8.54476e+04,
atom= 12730*
*
*
*Step 11, time 0.011 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 0.000184, max 0.002545 (between atoms 12731 and 12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12731 12730 63.6 0.0936 0.0937 0.0936*
*Step= 11, Dmax= 6.2e-02 nm, Epot= -9.23686e+05 Fmax= 1.13169e+05,
atom= 15031*
*Step= 12, Dmax= 7.4e-02 nm, Epot= -9.23888e+05 Fmax= 3.23226e+05,
atom= 15031*
*
*
*Step 13, time 0.013 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 0.054250, max 0.852392 <tel:0.852392> (between atoms 12731 and
12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12736 12728 142.1 0.1908 0.1192 0.1681*
* 12737 12728 146.1 0.1966 0.1354 0.1681*
*
*
*Back Off! I just backed up step13b_n4.pdb to ./#step13b_n4.pdb.1#*
*
*
*Back Off! I just backed up step13c_n4.pdb to ./#step13c_n4.pdb.1#*
*Wrote pdb files with previous and current coordinates*
*Step= 13, Dmax= 8.9e-02 nm, Epot= -9.22947e+05 Fmax= 2.12030e+06,
atom= 12728*
*Step 14, time 0.014 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 0.060515, max 0.946017 (between atoms 12731 and 12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12736 12728 141.9 0.1908 0.1315 0.1681*
* 12737 12728 149.5 0.1966 0.1435 0.1681*
*
*
*Back Off! I just backed up step14b_n4.pdb to ./#step14b_n4.pdb.1#*
*
*
*Back Off! I just backed up step14c_n4.pdb to ./#step14c_n4.pdb.1#*
*Wrote pdb files with previous and current coordinates*
*Step= 14, Dmax= 4.5e-02 nm, Epot= -9.25189e+05 Fmax= 2.68447e+06,
atom= 12728*
*
*
*Step 15, time 0.015 (ps) LINCS WARNING*
*relative constraint deviation after LINCS:*
*rms 1.882205, max 21.643097 (between atoms 12736 and 12728)*
*bonds that rotated more than 30 degrees:*
* atom 1 atom 2 angle previous, current, constraint length*
* 12730 12728 173.7 0.3265 3.7204 0.1681*
* 12731 12728 167.1 0.3272 3.6402 0.1681*
* 12736 12728 159.7 0.1315 3.8068 0.1681*
* 12737 12728 157.0 0.1435 3.7391 0.1681*
* 12731 12730 48.9 0.0913 0.1124 0.0936*
* 12737 12736 38.5 0.0960 0.1056 0.0936*
*
*
*Back Off! I just backed up step15b_n4.pdb to ./#step15b_n4.pdb.1#*
*
*
*Back Off! I just backed up step15c_n4.pdb to ./#step15c_n4.pdb.1#*
*Wrote pdb files with previous and current coordinates*
*Warning: 1-4 interaction between 12732 and 12741 at distance 1.975
which is larger than the 1-4 table size 1.800 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:*
* Connect Bonds of 7310 missing 1*
* U-B of 21832 missing 3*
* Proper Dih. of 35369 missing 12*
* LJ-14 of 36933 missing 10*
* exclusions of 151813 missing 20*
*
*
*-------------------------------------------------------*
*Program mdrun_d, VERSION 4.5.4*
*Source code file: domdec_top.c, line: 173*
*
*
*Software inconsistency error:*
*Some interactions seem to be assigned multiple times*
*For more information and tips for troubleshooting, please check the
GROMACS*
*website at http://www.gromacs.org/Documentation/Errors*
*-------------------------------------------------------*
*
*
*"Ich Bin Ein Berliner" (J.F. Kennedy)*
I tryed both with constrain then without, but I obtain always the same
result.
The files I have used to run the minimization can be downloaded from
http://160.80.35.105/download/vsite.tgz
Has anyone of you any idea?
Francesco
