[gmx-users] analysis the results of melocular dynamics simulation

[Javier Cerezo]

Hi Yeping

El 13/12/11 13:17, yp sun escribió:
> Dear Sir,
> I finished my simulation with gromacs, but whatever orders I use to 
> analysize the results, I always get errors. For example, when I type:
> g_density -f  md.trr
> It returns:
>
> Program g_density, VERSION 3.3.1
> Source code file: gmxfio.c, line: 706
> Can not open file:
> topol.tpr
>
You need a *.trp file: named topol.tpr by default, but you can set your 
particular one with -s label. What the error say is that the file 
"topol.tpr" either does not exists or has not the right permissions.

> When I type:
>  g_energy --f md.edr --o potential.xvg
> It returns:
> Program g_energy, VERSION 3.3.1
> Source code file: statutil.c, line: 799
> Invalid command line argument:
> --f
> When I type: g_rms --s md.tpr --f md.trr --o rmsd.xvg
> It returns:
> Program g_rms, VERSION 3.3.1
> Source code file: statutil.c, line: 799
> Invalid command line argument:
> --s
> When I type:
> g_gyrate --f md.trr --s md.tpr --o gyrate.xvg
> It retures:
> Program g_gyrate, VERSION 3.3.1
> Source code file: statutil.c, line: 799
> Invalid command line argument:
> --f
>
These three cases seem as a problem with the character "-", you using a 
differently encoded character (in your first example it is right however)

> I totally have no ideas about these error. I didn't get error 
> information when I do the simulation. I should I do with this situation?
> Thanks!
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>

-- 
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tlf.(+34)868887434

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