[gmx-users] mdrun error

[Pawan Kumar]

probably a bad starting structure...
check this website for  pressure scaling warning :
http://wiki.gromacs.org/index.php/Errors

regards,
pawan

On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora <sheetal.arora83 at gmail.com>wrote:

> I am trying to run the simulation of protein ligand complex.
> But after running the mdrun by giving command-"grompp –f md.
> mdp –c pr.gro –p trp.top –o md.tpr "
> and then "nohup mdrun –deffnm md & "
> the md.log file is showing the following message-
> Step 11  Warning: pressure scaling more than 1%, mu: 1.01684 1.01684
> 1.01684
>
> Step 13  Warning: pressure scaling more than 1%, mu: 0.947161 0.947161
> 0.947161
>
> Step 14  Warning: pressure scaling more than 1%, mu: 1.01207 1.01207
> 1.01207
>
> Step 15  Warning: pressure scaling more than 1%, mu: 1.18248 1.18248
> 1.18248
>
> Step 16  Warning: pressure scaling more than 1%, mu: 0.867467 0.867467
> 0.867467
>
> Step 16, time 0.032 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.099556 (between atoms 1396 and 1398) rms 0.028595
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>      21     23   30.8    0.1740   0.1569      0.1470
>      38     40   32.0    0.1740   0.1583      0.1470
>      54     56   33.0    0.1740   0.1588      0.1470
>      56     57   30.6    0.1810   0.1623      0.1530
>      67     69   31.4    0.1740   0.1568      0.1470
>     104    106   32.6    0.1740   0.1588      0.1470
>     106    107   31.1    0.1811   0.1632      0.1530
>     216    218   31.8    0.1741   0.1584      0.1470
> I am attaching my md.mdp file.Please help me in this regard.
>
> --
> Sheetal Arora
> M.Tech(Biotechnology & Medical Engg)
>
> NIT Rourkela
>
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