[gmx-users] problem in prest.mdp file

[Mark Abraham]

Bhawana Gupta wrote:
> hello everybody,
> I m sending this mail just to ask u problem which i m facing which using 
> command for grompp prest.mdp
> Error is
> Program grompp, VERSION 4.0
> Source code file: futil.c, line: 527
> 
> Fatal error:
> Library file posre.itp not found in current dir nor in default directories.
> (You can set the directories to search with the GMXLIB path variable)

That means what it says. You instructed grompp to expect a posre.itp 
file (which might normally be output by pdb2gmx and still be residing in 
your working directory) but grompp didn't find one.

> They are also saying that
> NOTE 1 [file *_md_water_prest.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.

That also means what it says. If it doesn't make sense, then you can 
start by doing some background reading on thermostats.

Mark