[gmx-developers] small bug in gmx solvate

[Mark Abraham]

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> 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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