[gmx-users] Lincs again

[Haberl Florian]

Hi

search gromacs mail archive, if your protein is not enough "relaxed" than
this will always appear, so do further energy minimisation and/ or
simulation with position restraining.

> hi again
>  similiar to the previous mail i am doing other simulation of other
> protein and again got tha same error
> with LINCS
>
> Constraint error in algorithm Lincs at step 973112
>
> Step 973113, time 1946.23 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 20.680283 (between atoms 1449 and 1451) rms 0.741946
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1429   1438   32.0    0.1571   0.1867      0.1530
>    1438   1439   37.8    0.1263   0.1525      0.1230
>    1438   1440   30.9    0.1318   0.1991      0.1330
>    1440   1441  100.1    0.0564   0.2241      0.1000
>    1440   1442  137.7    0.3441   0.7378      0.1470
>    1442   1443  152.1    0.4083   1.0938      0.1530
>    1442   1449  175.9    0.6039   1.8333      0.1530
>    1443   1444   95.7    0.5500   0.9234      0.1530
>    1444   1445   83.9    0.9134   0.6641      0.1230
>    1444   1446   86.0    0.1825   0.7594      0.1330
>    1446   1447   95.4    0.2018   0.1982      0.1000
>    1446   1448   96.6    0.3461   0.1610      0.1000
>    1449   1450  147.5    0.4649   1.9323      0.1230
>    1449   1451  153.6    0.4008   2.8835      0.1330
>    1451   1452  164.0    0.1313   1.9797      0.1470
>    1451   1455  164.5    0.2039   1.7734      0.1470
>    1452   1456   82.4    0.1670   0.6218      0.1530
>    1453   1454   59.0    0.1566   0.2983      0.1530
>    1454   1455   41.8    0.1490   0.5385      0.1530
>    1458   1459   88.5    0.1168   0.1112      0.1000
> Constraint error in algorithm Lincs at step 973113
>
> Step 973114, time 1946.23 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 5468.159180 (between atoms 1442 and 1449) rms 243.802231
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1422   1424   44.1    0.1473   0.2103      0.1470
>    1424   1425   79.9    0.1544   2.8279      0.1530
>    1425   1426   60.6    0.1215   2.8025      0.1230
>    1425   1427   92.2    0.1415   3.8149      0.1330
>    1427   1428   84.9    0.0994   4.5696      0.1000
>    1429   1430   73.3    0.1364  18.4517      0.1530
>    1429   1438   86.6    0.1870  74.3095      0.1530
>    1430   1431  151.4    0.1659   1.2032      0.1530
>    1432   1433   43.5
>
>
>
> etc etc
>
> What i am doing wrong
>
> this is may mdp file
>
> cpp                 =  /lib/cpp
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  25000000 ; total 100 ps.
> nstcomm             =  1
> nstxout             =  6000
> nstvout             =  6000
> ;nstfout             =  0
>
> nstxtcout           =  1000
> xtc_precision       =  1000
> xtc_grps            =  protein
>
> nstlist             =  5
>
> ;Energy Groups
> ;energygrps         =  protein ligand sol
> energygrps          =  protein sol
>
> ns_type                  = grid
> coulombtype              = cut-off
> rlist                    = 0.9
> rvdw                     = 1.4
> rcoulomb                 = 1.4
>
>
>
>
>
>
>
> ; Berendsen temperature coupling is on in three groups
> Tcoupl              =  berendsen
> tau_t               =  0.1      0.1    0.1
> tc_grps             =  protein  sol    NA+
> ref_t               =  300      300    300
>
> ; Pressure coupling is on
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
>
> ; Generate velocites is on at 300 K.
> gen_vel             =  no
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
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------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

------------------------------------------------------------------------