[gmx-users] gromacs doubt

[Justin A. Lemkul]

manjula kasinathan wrote:
> 
> Hi all
> 
>        i have done protein protein interaction and the complex structure 
> was taken for MD simulation using Gromacs. the length of the protein was 
> around 1100 aa. while performing mdrun step for position restrain i got 
> error. i have carried out mdrun for 1ps and the command given for mdrun 
> and position restrain are
> 
>          grompp -f *.pdb -c *.gro -p top.top -o *.tpr
> 
>          mdrun -v -deffnm pr
> 
> error i got was
> 
> starting mdrun '? in water'
> 500 steps,      1.0 ps.
> step 400, remaining runtime:   133 s         
> Step 416, time 0.832 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000577, max 0.008379 (between atoms 5530 and 5532)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    8190   8191   30.7    0.1014   0.1000      0.1000
> 
> Step 419, time 0.838 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000874, max 0.019432 (between atoms 5526 and 5527)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     112    113   31.0    0.1017   0.1002      0.1000
> 
> Step 430, time 0.86 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 158552932798158.562500, max 14888250728513536.000000 (between atoms 
> 1734 and 1735)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    4469   4471   66.7    0.1327   0.5535      0.1330
>    4469   4470   69.6    0.1227   0.5336      0.1230
> 
>   8001   8003   47.0    0.0999   0.0998      0.1000
>    7995   7996   30.0    0.1001   0.0999      0.1000
>    7970   7971   34.0    0.0999   0.1002      0.1000
> 
> t = 0.860 ps: Water molecule starting at atom 81142 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Wrote pdb files with previous and current coordinates
> 
> 
> could any one pls  help me to overcome this problem.how give me some ideas.
> 
> looking forward for a solution. thanx in advance.
> 
> 

Please consult the following:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

...as well as searching for this error in the mailing list archive.  You will 
find thousands of posts, doubtless some of them will provide you with some 
information.

If you want specific help, please post (at the very least) your .mdp file and 
describe any steps you have taken to construct and/or energy-minimize your 
structure.

-Justin

> 
> 
> 
> 
> -- 
> With Regards,
> 
> Manjulakasinathan
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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