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Dear Gromax developers,<br>
<br>
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.<br>
<br>
<br>
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,<br>
<br>
MODEL 1<br>
ATOM 0 O MOL 1 0.000 0.000 0.119 1.00
0.00 O <br>
ATOM 1 H MOL 1 0.000 0.763 -0.477 1.00
0.00 H <br>
ATOM 2 H MOL 1 0.000 -0.763 -0.477 1.00
0.00 H <br>
ENDMDL<br>
<br>
Then the program was stuck in a while loop, because the box in
solvate.cpp was null.<br>
<br>
<br>
In more details, I'm trying to do the tutorial present in this page<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf">http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf</a><br>
<br>
You can download the input files with the following link<br>
<a moz-do-not-send="true"
href="https://mbarbry.website.fr.to/nextcloud/index.php/s/Wts5ejbyp76ymDp">https://mbarbry.website.fr.to/nextcloud/index.php/s/Wts5ejbyp76ymDp</a><br>
<br>
Thus I have a Lysozyme protein, and I want to add a solvent around
it, therefore I used the command.<br>
<br>
gmx solvate -cs H2O-nocell.pdb -cp centered.gro -p topol.top
-o solvated.gro<br>
<br>
Where H2O-nocell.pdb is the file described above.<br>
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.<br>
<br>
Second problem, I then added a cell to the H2O.pdb file,<br>
<br>
MODEL 1<br>
CRYST1 8.0 10.0 8.0 90.00 90.00 90.00<br>
ORIGX1 1.000000 0.000000 0.000000 0.00000
<br>
ORIGX2 0.000000 1.000000 0.000000 0.00000
<br>
ORIGX3 0.000000 0.000000 1.000000 0.00000<br>
ATOM 0 O MOL 1 0.000 0.000 0.119 1.00
0.00 O <br>
ATOM 1 H MOL 1 0.000 0.763 -0.477 1.00
0.00 H <br>
ATOM 2 H MOL 1 0.000 -0.763 -0.477 1.00
0.00 H <br>
ENDMDL<br>
<br>
<br>
The program goes a bit further but then return a memory error<br>
<br>
Removed 0 solvent atoms due to solvent-solvent overlap<br>
Removed 120 solvent atoms due to solute-solvent overlap<br>
<br>
Program received signal SIGSEGV, Segmentation fault.<br>
0x00007ffff7027dd7 in
gmx::internal::AnalysisNeighborhoodSearchImpl::~AnalysisNeighborhoodSearchImpl()<br>
() from /home/marc/.local/gromacs/lib/libgromacs.so.3<br>
(gdb) quit<br>
<br>
<br>
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 <a moz-do-not-send="true"
href="http://avogadro.cc/">Avogadro</a> and <a
moz-do-not-send="true"
href="https://wiki.fysik.dtu.dk/ase/index.html">ASE</a>, but
obviously they were not think to be use with Gromacs.<br>
<br>
Thanks for your helps,<br>
<br>
Best regards,<br>
Marc Barbry<br>
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