[gmx-users] R: Re: rhombic dodecahedron and g_sas

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 14 01:38:03 CEST 2011

On 14/07/2011 1:08 AM, Anna Marabotti wrote:
> In any case, if I understand well, I have to convert my .gro file (into a
> .tpr file to obtain the exact value of hydrophobicity/hydrophilicity, right?

You should be able to use the .tpr which which you generated the 
trajectory. One doesn't "convert" a coordinate file into a .tpr file - a 
large amount of information is compiled with the coordinates by grompp.

> And what about the warning on possible "erroneous results" for
> non-rectangular boxes? Is there a way to understand if the results are
> reliable or not?

Not without someone reading the code - but trjconv centering the protein 
avoids the issue regardless of box shape.


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