I am trying to build a slab of silicate as an infinite molecule,
eventually run run with water and solutes. A picture of what I'm trying
to build is located at www.chemistry.ohio-state.edu/~singer/md
There are many posts to gmx-users with uses having similar problems with
infinite, periodically replicated molecules. Unfortunately, I can't
seem to figure this one out from those previous posts.
Also unfortunate is that this message is so long, that I feel compelled
to give a table of contents:
1) Description of symptoms
2) Is David van der Spoel's pbc = full the only way? How to implement?
3) Is my procedure for making the topology file correct?
Thanks in advance for helping this newbie.
Sherwin Singer
---------------------------------------------------------------------------
1) Symptoms
Running bash shell, I have "declare -x GMXFULLPBC=1", and I set "pbc =
xyz" in the mdp file.
I do not get any "inconsistent shift" errors from grompp under these
conditions.
I tried to run md with very small time steps (0.0002 ps) and low
temperature (20K). I first get the error,
"Warning: 1-4 interaction at distance larger than 2.25
These are ignored for the rest of the simulation"
then a few of the following
"Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc."
and finally
"Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]"
I also failed to get energy minimization to work.
2) David van der Spoel's pbc = full
Searching the gmx-users archives, I found a very interesting post,
http://www.gromacs.org/pipermail/gmx-users/2003-September/033572.html ,
where David van der Spoel writes that pbc = full may be necessary. Is
it the only way? Presently I am using Gromacs 3.1.4 installed with
rpm's. (I had trouble compiling on RH 9.0.) If necessary, I will build
a later version.
3) Perhaps my procedure for making the topology file is wrong.
The [ bonds ] and [ angles ] list seemed straightforward. To generate
the [ pairs ] and [ dihedrals ] lists I listed all unique 1-2-3-4 walks
through the crystal and listed each one under [ dihedrals ]. Then I
took the 1-4 members of each of those walks and listed them under [
pairs ], and I'm using the parameters for those 1-4 interactions from
the ffgmx files. I was a little unsure about this last step, because in
the discussion of the [ dihedrals ] section of the urea example (page
103 of the 3.1.1 Gromacs manual), it says to "do not forget to erase
the 1-4 interactions in [ pairs ]!!" What does this mean?
Also, I assigned charges to all the SI, OS, OA and HO atoms of my chunk
of silicate. I could not find default charge parameters in the force
field.
--
Sherwin J. Singer
Department of Chemistry
Ohio State University
Columbus OH, 43214
singer at chemistry.ohio-state.edu
614-292-8909
614-292-1685 (fax)