[gmx-users] position restrain dynamics error

[Justin Lemkul]

On 5/8/13 3:07 AM, Subramaniam Boopathi wrote:
> Dear Sir,
>          I am succesfully run molecules upto energy minimization, in case of
> position restrain md step , i have following, could you help to overcome
> the A charge group moved too far between two domain decomposition steps.
>
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.021061, max 0.387149 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.0    0.0960   0.1332      0.0960
>
> Step 2, time 0.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.034712, max 0.636602 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.1    0.1332   0.1571      0.0960
>
> Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1#
>
> Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1#
> Wrote pdb files with previous and current coordinates
>
> Step 3, time 0.006 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.023755, max 0.423951 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.0    0.1571   0.1367      0.0960
>
> Step 4, time 0.008 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.051081, max 0.931870 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.3    0.1367   0.1855      0.0960
>
> Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1#
>
> Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1#
> Wrote pdb files with previous and current coordinates
>
> Step 5, time 0.01 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.020335, max 0.372790 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   89.9    0.1855   0.1318      0.0960
>
> Step 6, time 0.012 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.056021, max 1.029913 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.2    0.1318   0.1949      0.0960
>
> Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2#
>
> Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2#
> Wrote pdb files with previous and current coordinates
>
> Step 7, time 0.014 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.024586, max 0.451876 (between atoms 360 and 363)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      360    363   90.0    0.1949   0.1394      0.0960
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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