On 7/02/2012 2:26 AM, Qinghua Liao wrote:
Dear GMX users,
We are trying to do a simulation of a protein attached to a small
molecules, how should I do to setup the system? For the parameters of
the small molecule, I got it from ATB sever, however I don't know how
to bond the small molecule and the N terminal of protein.
The general solution is to use
http://www.gromacs.org/Documentation/File_Formats/specbond.dat to allow
pdb2gmx to learn about the bond to the new molecule. As you will see in
your [bonds] section, you have no bond to your new residue.
For gro file, it is ok, but for the topology file, I tried to merge
the parameters of small molecule and the topology file together, and
then renumber the atom number, and the grompp worked. But when I
wanted to do the geometry optimization, it did not work. Here is the
error:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with
the given box and a minimum cell size of 3.52902 nm
http://www.gromacs.org/Documentation/errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
You have set up your "small" molecule with only three charge groups.
mdrun functions as a large number of loops over interactions between and
within charge groups. The size of your large charge groups creates a
large lower bound on the number of atoms that have to be present on each
processor of a parallel simulation, and your number of molecules is
unsuitable for this. You need to investigate how to generate charge
groups that are both smaller and consistent with the force field.
Mark
I guess it is still a problem of the setup of the system, the
attachments are the gro and top files for the system. So could someone
give me some suggestions? Thanks very much!
--
Best Regards,
Qinghua
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