[gmx-users] Lincs again

Kai Zhuang kai.zhuang at gmail.com
Thu May 12 19:37:52 CEST 2005


hi,
i' new to Gromacs and MD (only been looking at it for a week)
i have a question about ur mdp script...
>dt                  =  0.002    ; ps !
> nsteps              =  25000000 ; total 100 ps.
how is 25000000 * 0.002 = 100?  the unit is ps right?
thx
Kai

On 5/12/05, Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu> wrote:
> 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
> >>
> >>
> >>_______________________________________________
> >>gmx-users mailing list
> >>gmx-users at gromacs.org
> >>http://www.gromacs.org/mailman/listinfo/gmx-users
> >>Please don't post (un)subscribe requests to the list. Use the
> >>www interface or send it to gmx-users-request at gromacs.org.
> >>
> >>
> >>
> >
> >
> >------------------------------------------------------------------------
> > Florian Haberl              Universitaet Erlangen/Nuernberg
> > Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
> >
> > Mailto: florian.haberl AT chemie.uni-erlangen.de
> >
> >------------------------------------------------------------------------
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
> >
> >
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> 


-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789



More information about the gromacs.org_gmx-users mailing list