[gmx-users] LINCS problem with EM and Virtual sites

[francesco oteri]

Hi gromacs users,
I am tying to minimize a protein through grolacs 4.5.5 double precision.
If I try to minimize it without virtual site, everythin goes fine but if I
add virtual site through:

pdb2gmx -vsite hydrogens -chainsep id -f Aqui_model.pdb  -ff charmm27
 -water tip3p -posrefc 1000 -v -rtpres
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 (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
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