[gmx-users] mdrun error

[Justin A. Lemkul]

Check out the wiki at:

http://wiki.gromacs.org/index.php/Errors#LINCS_warnings

Alternatively, search the list for some of my posts from around a year ago - NVT
and minimization of a lipid bilayer (or search for my name, they should come up
as well).  I suspect you have bad contacts in your starting structure.

-Justin

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
> hi i am trying to run mdrun for protein in membrane system. When i run mdrun
> i get a warning
>
> Step -2, time -0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 2.144082 (between atoms 12433 and 12434) rms 0.216090
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   11761  11762   90.0    0.1633   0.2387      0.1000
>   11929  11930   31.7    0.1633   0.1000      0.1000
>   12097  12098   90.0    0.1632   0.1041      0.1000
>   12265  12266   90.0    0.1633   0.2266      0.1000
>   12433  12434   90.0    0.1633   0.3144      0.1000
> starting mdrun 'alamethicin in popc'
> 500 steps,      0.5 ps.
>
> Warning: 1-4 interaction between 115 and 136 at distance 1.144 which is
> larger t
> han the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max inf (between atoms 12007 and 12008) rms inf
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>   11619  11620   90.0    0.1000   0.1411      0.1000
>   11633  11634   90.0    0.1000 13155507200.0000      0.1000
>   11640  11641   90.0    0.1000   0.1214      0.1000
> .....
>   12619  12620   90.0    0.1080   0.1447      0.1080
> Wrote pdb files with previous and current coordinates
> step 0Segmentation fault
> I am using shake in my mdp file. I want to restrain water.
>
> my mdp file is:
> title                = popc128a
> integrator           = md
> define               = -DFLEX_SPC
> dt                   = 0.001
> nsteps               = 500
> nstxout              = 500
> ns_type              = grid
> pbc                  = xyz
> constraints          = hbonds
> constraints_algorithm= shake
> coulombtype          = PME
> vdwtype              = cut-off
> rcoloumb             = 1.0
> nstlist              = 10.0
> Tcoupl               = no
> pcoupl               = no
> compressibility      = 4.5e-5
> gen_temp             = 300
> gen_vel              = no
> Please help.
> Thanks in advance.
> _________________________________________________________________
> Check out some new online services at Windows Live Ideas—so new they haven’t
> even been officially released yet.
>
http://www.msnspecials.in/windowslive/_______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



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

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/

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