[gmx-users] NPT

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear All
> In doing umbrella sampling ,when I want to generate NPT every thing is
> going well but one error is occuring in the first.
> please let me know how can  I solve this problem.
> Is it usefull to extend the degree which is defined in .mdp file?

No.  The constraints are failing, but they are not the problem that needs to be 
fixed.  Please see:

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

-Justin

> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
> 
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1504.051113, max 55378.273438 (between atoms 5289 and 5290)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    5264   5263   40.6    0.1143   0.1260      0.1140
>    5293   5294   82.7    0.1221 2613.7048      0.1090
>    5291   5293   77.2    0.1517 6084.3052      0.1390
>    5291   5292  101.0    0.1117 1519.0425      0.1090
>    5289   5291   87.7    0.1353 6893.7969      0.1390
>    5289   5290   88.4    0.1437 7531.5815      0.1360
>    5289   5287   88.4    0.1456 7542.5801      0.1390
>    5287   5288   89.7    0.1092 381.6111      0.1090
>    5285   5287   92.3    0.1395 355.0215      0.1390
>    5285   5286  123.8    0.1101  44.8588      0.1090
>    5284   5293   89.0    0.1478 4606.4570      0.1390
>    5284   5285   79.3    0.1402 173.6082      0.1390
>    5278   5279   78.9    0.1529   1.1246      0.1530
>    5277   5278  122.9    0.1545  13.1470      0.1530
>    5276   5284   84.9    0.1422 159.0514      0.1390
>    5276   5277   68.4    0.1543  90.8518      0.1530
>    5276   5275   39.5    0.1439  72.5391      0.1430
>    5274   5275  103.7    0.1436  21.6098      0.1430
>    5273   5274  108.6    0.1394   3.3410      0.1390
>    5276   5272   45.7    0.1402  80.7004      0.1390
>    5272   5273  127.3    0.1340  14.2414      0.1330
>    5272   5270   69.8    0.1336  12.6282      0.1330
>    5270   5271  113.3    0.1092   0.2532      0.1090
>    5268   5270  104.5    0.1391   0.2727      0.1390
>    5268   5269   44.0    0.1091   0.1624      0.1090
>    5273   5266   58.5    0.1342  14.0148      0.1330
>    5265   5268   36.7    0.1394   0.1774      0.1390
> 
> Actually md is crush,of course I think so.
> Thanks in advance

-- 
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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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