[gmx-users] Lincs again

[Osmany Guirola Cruz]

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