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