[gmx-users] gromacs doubt

[Chandan Choudhury]

Have a loolk at
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings


Chadnan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, May 13, 2010 at 10:34 AM, manjula kasinathan <manjubfs at gmail.com>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.
>
>
>
>
>
> --
> With Regards,
>
> Manjulakasinathan
>
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