[gmx-users] mdrun error

[pragya chohan]

----------------------------------------> Date: Fri, 9 Nov 2007 09:01:48 -0500> From: jalemkul at vt.edu> To: gmx-users at gromacs.org> Subject: Re: [gmx-users] mdrun error>> 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 :>>>>> 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/>> =========================================================> _______________________________________________> 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

Thanks for your help. I figured the problem out but am getting an error again. I have alamethicin in popc and water. Since alamethicin has some non standard residue i made topology file in text editor and ran mdrun with only alamethicin. It went fine. But when i am tring to minimize alamethicin in popc mdrum probably does not recognize the starting of second chain and gives me following error:

Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is larger than 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=    1, Dmax= 1.0e-02 nm, Epot=  3.25524e+09 Fmax= 1.00321e+09, atom= 2441
Step=    2, Dmax= 1.2e-02 nm, Epot=  2.21743e+09 Fmax= 1.82388e+08, atom= 12852
Step=    3, Dmax= 1.4e-02 nm, Epot=  1.95672e+09 Fmax= 7.44135e+07, atom= 262
Step=    4, Dmax= 1.7e-02 nm, Epot=  1.88109e+09 Fmax= 4.32188e+07, atom= 260
Step=    5, Dmax= 2.1e-02 nm, Epot=  1.84989e+09 Fmax= 2.77292e+07, atom= 262
Step=    6, Dmax= 2.5e-02 nm, Epot=  1.83083e+09 Fmax= 1.89783e+07, atom= 258
Step=    7, Dmax= 3.0e-02 nm, Epot=  1.81606e+09 Fmax= 9.97167e+06, atom= 253
Step=    8, Dmax= 3.6e-02 nm, Epot=  1.79660e+09 Fmax= 2.09557e+07, atom= 258
Step=    9, Dmax= 4.3e-02 nm, Epot=  1.78793e+09 Fmax= 1.63547e+07, atom= 259
Step=   10, Dmax= 5.2e-02 nm, Epot=  1.77532e+09 Fmax= 7.54157e+06, atom= 12539
Step=   11, Dmax= 6.2e-02 nm, Epot=  1.74488e+09 Fmax= 7.42417e+06, atom= 12539
Step=   12, Dmax= 7.4e-02 nm, Epot=  1.70998e+09 Fmax= 7.28331e+06, atom= 12539
Step=   13, Dmax= 8.9e-02 nm, Epot=  1.66920e+09 Fmax= 7.11508e+06, atom= 12539
Wrote pdb files with previous and current coordinates

Back Off! I just backed up step13.pdb to ./#step13.pdb.1#

Back Off! I just backed up step14.pdb to ./#step14.pdb.1#
Wrote pdb files with previous and current coordinates

my pdb file at 164 to 169 is:
ATOM    164  CZ  PHL    21      44.000  52.840  35.170  1.00  0.00
ATOM    165  HZ  PHL    21      44.990  53.260  35.090  1.00  0.00
ATOM    166  CX  PHL    21      38.140  50.450  37.160  1.00  0.00
ATOM    167  OY  PHL    21      37.940  49.350  38.060  1.00  0.00
ATOM    168  HY  PHL    21      37.040  48.940  37.950  1.00  0.00
ATOM    169  CA  ACE    22      53.840  44.410  66.930  1.00  0.00

I think it is not recognising different chain. Am i right? Please help me.
_________________________________________________________________
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