[gmx-developers] small bug in gmx solvate

[Marc Barbry]

Thanks for the links, I will have a look.

Marc

On 25-05-18 16:15, Mark Abraham wrote:
> Hi,
>
> Thanks for your interest! On this list we try to discuss issues about 
> how to develop with GROMACS or for GROMACS. If there's a known bug, as 
> it looks like you have, then opening at issue at 
> https://redmine.gromacs.org would be a very welcome start 
> (particularly mentioning details of which GROMACS version and 
> attaching tarballs input files).
>
> Generating initial coordinate files is a better question for the 
> gmx-users mailing list. What tools you might want depend on lot on 
> what you're trying to do. While there's a partial list at 
> http://www.gromacs.org/Downloads/Related_Software, others doing 
> projects similar to yours will tend to have better suggestions than 
> the developers!
>
> Mark
>
> On Fri, May 25, 2018 at 4:09 PM Marc Barbry <marc.barbry at mailoo.org 
> <mailto:marc.barbry at mailoo.org>> wrote:
>
>     Dear Gromax developers,
>
>     First of all, I would like to indicate that I'm a new user of
>     Gromacs, therefore some of my comments/questions may be basics.
>     Furthermore, it seems that I'm not using the right method to do
>     what is explained below, if you could indicate me a better
>     technique to realize this it would greatly help me.
>
>
>     Running the gmx solvant program, I detected a bug related to the
>     input. When using a basic pdb file for water containing only the
>     coordinates of the atoms,
>
>     MODEL     1
>     ATOM      0    O MOL     1       0.000   0.000   0.119 1.00 
>     0.00           O
>     ATOM      1    H MOL     1       0.000   0.763  -0.477 1.00 
>     0.00           H
>     ATOM      2    H MOL     1       0.000  -0.763  -0.477 1.00 
>     0.00           H
>     ENDMDL
>
>     Then the program was stuck in a while loop, because the box in
>     solvate.cpp was null.
>
>
>     In more details, I'm trying to do the tutorial present in this page
>     http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf
>
>     You can download the input files with the following link
>     https://mbarbry.website.fr.to/nextcloud/index.php/s/Wts5ejbyp76ymDp
>
>     Thus I have a Lysozyme protein, and I want to add a solvent around
>     it, therefore I used the command.
>
>          gmx solvate -cs H2O-nocell.pdb  -cp centered.gro  -p
>     topol.top -o solvated.gro
>
>     Where H2O-nocell.pdb is the file described above.
>     In this case the program get stuck in the while loop line ~250 of
>     solvant.cpp because box[d][d] = 0.0. Obviously, a check of the box
>     is missing here in order to avoid such kind of issue, which are
>     difficult to debug.
>
>     Second problem, I then added a cell to the H2O.pdb file,
>
>     MODEL     1
>     CRYST1      8.0   10.0   8.0  90.00  90.00  90.00
>     ORIGX1      1.000000   0.000000  0.000000 0.00000
>     ORIGX2      0.000000   1.000000  0.000000 0.00000
>     ORIGX3      0.000000   0.000000  1.000000        0.00000
>     ATOM      0    O MOL     1       0.000   0.000   0.119 1.00 
>     0.00           O
>     ATOM      1    H MOL     1       0.000   0.763  -0.477 1.00 
>     0.00           H
>     ATOM      2    H MOL     1       0.000  -0.763  -0.477 1.00 
>     0.00           H
>     ENDMDL
>
>
>     The program goes a bit further but then return a memory error
>
>     Removed 0 solvent atoms due to solvent-solvent overlap
>     Removed 120 solvent atoms due to solute-solvent overlap
>
>     Program received signal SIGSEGV, Segmentation fault.
>     0x00007ffff7027dd7 in
>     gmx::internal::AnalysisNeighborhoodSearchImpl::~AnalysisNeighborhoodSearchImpl()
>         () from /home/marc/.local/gromacs/lib/libgromacs.so.3
>     (gdb) quit
>
>
>     I guess my input file is not correctly constructed, I'm a newbie
>     with pdb files and MD in general. Do you know a good way to
>     generate pdb file? At the moment I use Avogadro
>     <http://avogadro.cc/> and ASE
>     <https://wiki.fysik.dtu.dk/ase/index.html>, but obviously they
>     were not think to be use with Gromacs.
>
>     Thanks for your helps,
>
>     Best regards,
>     Marc Barbry
>     -- 
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