[gmx-users] Re:pdb2gmx - gromacs 3.2

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Tue Feb 17 10:33:01 CET 2004

Hi Wei Fu,

You should be aware that using a tight fitting box as you'll get when 
using the -princ option of editconf, the protein may reorient during the 
simulation and see its images. You should use a method to constrain 
rotational and translational motions then. But if you do, you might as 
well choose to make your box even tighter and base it on the geometry of 
your protein. We have a program to construct such a box. If you would 
like to use it, you can send me a coordinate file. Shortly we will make 
it available as a web service, but for now, I can do it like this (as 
long as not everybody is going to throw their structures at me). You 
should not expect too large conformational changes during the run, 
otherwise the changes of making it work will be less. The savings are on 
average 50% (wrt rhombic dodecahedron), but usually more for more 
irregular shapes.



Wei Fu wrote:

>Hi, I have the same pdb2gmx problem when using Gromacs3.2. just copy
>FF.dat from previous version, it works.
>The other problem is that when I using "editconf -f $file.gro -o
>$file2.gro -d 1.0
>some atoms is out of box when using both gromacs3.1.4 and gromacs3.2
>So, I try to using "editconf -f input.gro -princ -o output.gro -d 1.0"
>by gromcas3.2 to solve it, while
>I found the output.gro file is totally wrong, but when I use gromacs3.1.4
>do the same thing, it generates the correct coodinate. But it still
>has some atoms outside the box. The reason is that my protein has abnormal
>Should I use -c x y z to ajust box's position? Among them, x y z is a
>dummy point that is not the coordinate of atom. Any hit is appreciated.
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