[gmx-users] infinite molecule problems

Sherwin J. Singer singer at chemistry.ohio-state.edu
Tue Sep 30 21:10:01 CEST 2003

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

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

Sherwin J. Singer
Department of Chemistry
Ohio State University
Columbus OH, 43214
singer at chemistry.ohio-state.edu
614-292-1685 (fax)

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