[gmx-users] mdrun error

[Justin A. Lemkul]

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

Also,

compressibility     =  4.575e-4

is of the wrong magnitude for water.  Should be e-5.

-Justin

> regards,
> pawan
> 
> On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora 
> <sheetal.arora83 at gmail.com <mailto: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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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