[gmx-users] Re: LINCS warning:relative constraint deviation after LINCS:

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  You are
far more likely to reach someone with helpful ideas if you send your question
out to everyone, and the thread will be archived for others to benefit from in
the future.  Also, search this archive thoroughly for potential solutions to
your problem.  There are dozens of posts related specifically to LINCS warnings
with membranes.

For information about what a LINCS warning means, refer to the wiki:

http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

Probably your EM step did not resolve all bad contacts present in your system. 
Also, your .mdp file has a problem - never couple solvent and ions to different
temperature coupling groups!  This may or may not be part of your problem, but
is likely to cause headaches at some point.  Refer here:

http://wiki.gromacs.org/index.php/thermostats

In the absence of any other information (how you prepared your system, what you
have tried to do to resolve this issue), I can't comment further.  Hopefully
some of this information is useful.

-Justin

Quoting ÄÇÃÀÈÙ <nmr at mail.ccnu.edu.cn>:

> Dear Justin,
>    I am simulating a system with 5 peptide and a POPC membrane with gromacs .
> I
> have ran em succefully.But when I ran pr ,I got a LINCS warning:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 163.380417 (between atoms 25353 and 25354) rms 3.650424
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   25030  25038   34.0    0.1531   0.2013      0.1530
>   25038  25039   40.2    0.1231   0.1764      0.1230
>   25038  25040   71.3    0.1332   0.2284      0.1330
>   25040  25041   73.8    0.1001   0.1599      0.1000
>   25040  25042   80.5    0.1473   0.8682      0.1470
>   25042  25043   78.5    0.1542   2.2823      0.1530
>   25042  25055   80.1    0.1532   0.7523      0.1530
>   25043  25044   83.0    0.1539   5.5148      0.1530
>   25044  25045   80.8    0.1400   4.4305      0.1390
>   25044  25047   87.1    0.1399  17.3262      0.1390
>   25045  25046   71.4    0.1086   1.0713      0.1080
>   25047  25048   88.4    0.1087  14.2386      0.1080
>   25047  25051   88.2    0.1395  12.5692      0.1390
>   25049  25050   75.3    0.1083   1.1422      0.1080
>   25049  25053   85.5    0.1393   3.1301      0.1390
>   25051  25052   86.7    0.1082   6.8091      0.1080
>   25051  25053   85.9    0.1393   5.9519      0.1390
>   25053  25054   86.3    0.1082   3.6976      0.1080
>   25055  25056   71.8    0.1231   0.1754      0.1230
>   25055  25057   65.8    0.1331   0.2104      0.1330
>   25057  25058   39.9    0.1000   0.1405      0.1000
>   25057  25059   36.1    0.1470   0.1931      0.1470
>   25349  25350   78.9    0.1536   1.6355      0.1530
>   25350  25351  163.3    0.1604   1.8178      0.1530
>   25351  25352   43.4    0.1599   5.4292      0.1530
>   25352  25353   97.7    0.1578  24.5403      0.1530
>   25353  25354   83.2    0.1540  24.1639      0.1470
>   25354  25355  109.9    0.1098   3.5962      0.1000
>   25354  25356  108.3    0.1098   3.7714      0.1000
>   25354  25357   93.3    0.1098   5.5208      0.1000
> Constraint error in algorithm Lincs at step 0
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>     1.45008e+04    6.21453e+03    3.41089e+03    1.62397e+03    5.10741e+03
>      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. recip.
>     2.74078e+04    5.90825e+06   -4.65849e+03   -1.40426e-05   -1.04918e+07
>  Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
>     2.32371e+01   -4.52991e+06    3.69314e+09    3.68861e+09    1.66285e+07
>  Pressure (bar)
>     9.25953e+07
>
>
> Step 1  Warning: pressure scaling more than 1%, mu: 3.77786 3.77786 3.77786
>
> Step 1, time 0.001 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> ....................
> My popc_5ggn_pr.mdp and popc_5ggn.top are attacted below.I don't know where
> is
> wrong.Your advice is appreciated. Thank you very much.
>
> Best regards.
> wumin
> china  HuaZhong Normol University
>
>
>
>
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================