[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