Hi dear Gromacs users,<br>
<br>
I need some help in my simulation. I am trying to put in a
cubic box a protein next to an ice plane and then i solvate the system
and try to run the simulation. As the pdb2gmx doesntī work with water
molecules, I proceeded as the following: <br>
First I used the pdb2gmx
only with the protein to get a topology file.
Then I tried to create an .itp file of the ice molecules,
and for that I used the water model spc.itp (but I changed the
nomenclature in the file, everything that was called SOL I changed and
called OHH). <br>
Later I included this .itp file in the topology file,
paying attention to the number of molecules. After that I
used editconf to create a box and genbox to solvate
the system (From the .gro file with the protein next to the ice plane).
By this way in the topology was included the water molecules (called
SOL) by the .itp file of the water. Then in the parameter file I tried
to establish differences between the ice and water molecules by
applying frozen groups options to the OHH molecules.<br>
However the funny thing is that when I first used part of
the ice plane (with only 26 molecules that were somehow far away from
the protein) the simulation finished, but when I used the
whole plane (round 1200 molecules) the simulation crashes in no more
than 5 or 10 steps.<br>
<br>
The message is always like this : <br>
Fatal error: Number of grid cells is zero. Probably the system and box collapsed.<br>
<br>
And there are warnings like:<br>
1-4 interactions between 25 and 33 at distance 1,322 which
is larger than the 1-4 table size 1 nm, This usually means your system
is exploding.<br>
<br>
<br>
I tried to increase the table size but as I
increased this value the distance always increased together, and I got
agai the same warning with different values, so this didnīt help.
I tried also to perform energy minimization before solvating the
system, but something bizarre happened, part of the ice plane just
changed position with the protein... like the visualization was the
same, but water molecules were in the position where the protein was
and the protein was in the position where these water molecules
were before.<br>
<br>
I tried then to put he whole protein a little bit far away
from the plane to see what happens, and when I runned the simulation
(without energy min.) the same birarre thing happened (part of the
plane changed place with the protein).<br>
<br>
I am still a begginer in Gromacs, and I really donīt know
what could be the reason for these errors... It is also the first time
that I am dealing with molecular dynamics simulation. Someone wrote me
that it could be something related to topologies, but i really couldnīt
find where the error was. So I ask for your kindness help. Suggestions
and advices will be welcome,<br>
<br>
Best regards,<br>
Fernando Mattio<br>
<br>
<br>
<br>