[gmx-users] Lincs again

[Osmany Guirola Cruz]

I understand that but the initial structure i got from a previous 
simulation (30ns) that crash because
lot of LINCS warnings then i got the final structure do a minimization 
and then crash again after 2ns
my question is Why happens after 30ns its a big time?
i will try your suggestion?


Thanks

Osmany




Haberl Florian wrote:

>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
>
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