[gmx-users] Simulation Box break into 16 domains => .tpr file is wrong (Gromacs 3.3.3)

[Chih-Ying Lin]

Hi
Tsjerk gave me suggestion to check the .tpr file created by the command
grompp.


*Energy minimization of the solvated system*

pbc = xyz (minim.mdp)

grompp_mpi -np 16 -v -f minim.mdp -c 6LYZ-solvated.gro -p 6LYZ.top -o
6LYZ-EM-solvated

mpiexec -np 16 mdrun_mpi -v -deffnm 6LYZ-EM-solvated



I early prepared for *6LYZ-solvated.gro* and then run the command grompp to
create 6LYZ-EM-solvated.tpr.
Next, run the command   *editconf -f  **6LYZ-EM-solvated.tpr -o
 6LYZ-EM-solvated-after-grompp.gro*
**
Use, VMD to visualize both *6LYZ-solvated.gro*     and     *
6LYZ-EM-solvated-after-grompp.gro*

*6LYZ-solvated.gro     => all molecules are intact * and protein is
centered.
*6LYZ-EM-solvated-after-grompp.gro  => protein and water molecules are
broken.*
**
**
This is the main problem that my simulation box into 16 domains.

Thank you
Lin



**
**
**


Chih-Ying Lin wrote:
>
> Hi
>  From the Gromacs Manual,
> http://manual.gromacs.org/current/online/editconf.html
> editconf =>
> The box can be modified with options -box, -d and -angles. Both -box and
> -d will center the system in the box.
>
> so, without -c option, the protein is already centered in the box.
> and, there is no description in the manual that people cannot use -d and
> -box simultaneously.
>
The manual cannot possibly warn against everything that people may try to
do.
Consider the function of these two options.  By using -d, editconf will
determine a suitable box size based on the dimensions of the solute.  By
using
-box, you are specifying the box vectors, which completely negates the
purpose
of using -d.  Perhaps the language in the manual is not clear.  Both -d and
-box
may center the solute, but *not* by simultaneously using -box and -d,
because
they can counteract each other.  In the absence of a warning, something odd
might be going on; we must eliminate this possibility in order to help you
better.
I would still suggest using a properly-formed command, with or without -c,
to
make sure that nothing is breaking down there.  The workflow you posted
before
seems reasonable enough, so something early on is probably breaking down.
Is
there any reason you minimized your protein without PBC?  What was the box
size
used in this EM step?  Usually an in vacuo EM is simply accomplished by
using a
huge box and plain cutoffs.  Solution EM would use a suitable box (with
editconf
-d *or* editconf -box) and better electrostatics methods.
-Justin
> I visualized the .gro file created by the editconf,  the protein is
> centered in the box as I can see.
>
> Thank you
> Lin
>
>
>
>
>
>
> Chih-Ying Lin wrote:
>  >
>  >
>  >
>  > Hi
>  > As I posted the command list earlier, to create the box
>  > editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75
>  > -box 6.0 6.0 6.0
>  >
>  >
>  > So, I think Justin's case is not the same as mine.
> Mark already pointed out that your command line is malformed.  You
> cannot use -d
> and -box simultaneously.  They are mutually exclusive.  You are also not
> centering the protein in the box (you are not using the -c option).  So,
in
> fact, what you're doing was exactly what my problem was - not centering
and
> potentially defining the box incorrectly.
> I would suggest that you at least try rebuilding your system, because
> the above
> command is certainly wrong.
> -Justin
>  > Thank you
>  > Lin
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