[gmx-users] Preparing a silicon bulk

Kevin C Chan cchan2242-c at my.cityu.edu.hk
Fri Dec 19 05:46:46 CET 2014

Due to some reasons I could not receive digests from the list so I could
only copy and paste from the archives and reply to you. I really hope this
reply could go to the same thread of my question so it would not screw the
list archive.

Back to the question, first thank you so much for your reply Justin. I
understand that pdb2gmx might not be useful, I just tried it. g_x2top seems
better but I could not get it work even following the file format: it says
it could find 1 name to type translations but it can not find forcefield
for atoms like

Opening force field file
There are 2 name to type translations in file gromos54a7.ff
Generating bonds from distances...
atom 8
Can not find forcefield for atom SI1-1 with 0 bonds
Can not find forcefield for atom SI2-2 with 0 bonds
Can not find forcefield for atom SI3-3 with 0 bonds
Can not find forcefield for atom SI4-4 with 0 bonds
Can not find forcefield for atom SI5-5 with 0 bonds
Can not find forcefield for atom SI6-6 with 0 bonds
Can not find forcefield for atom SI7-7 with 0 bonds
Can not find forcefield for atom SI8-8 with 0 bonds

I gave the n2t like

SI   SI         1     28.08   3    SI 2.352     SI 2.352      SI 2.352
 ;2.352 is measured from my input coordinates

and just trying with 8 SI atoms and in the future I definite would like to
have more.

While waiting for your comments on this g_x2top problem, I would also like
to have suggestions on manually writing the top file. As I don't think we
need those tedious dihedrals for a silicon bulk, I though the topology
should look rather simple:

#include "gromos54a7.ff"
; I have looked into gromos54a7 and found parameters for SI so this include
is enough am I right?
[ moleculetype ]
; name SomeName
SI 8
[ atoms ]
1  SI  1  SI  SI1  1  charge1
2  SI  1  SI  SI1  1  charge2
8  SI  1  SI  SI1  1  charge8
; Maybe bonds and angles are also needed? I am not sure
#include "spc.itp"
[ system ]

[ molecules ]
SI 8
SOL 100

Is this the case?

Thanks in advance,


On 12/18/14 12:38 PM, Kevin C Chan wrote:
> Dear Users,
> I wish to simulate a Silicon bulk using Gromacs. I have created the bulk
> using a plugin in VMD but I found difficulties when generating a top file
> from this pdb file. I have tried pdb2gmx and x2top but both does not work.
> Gromacs tells me that although we already have parameters for SI in maybe
> ffnonbonded.itp, we do not have SI in the residue topology database and
> ffbonded.itp. How could it be and I do appreciate if anyone could share
> experience of simulating a silicon bulk in Gromacs.

pdb2gmx is not the answer, since it was designed for linear polymers with
limited branching.  The only option for materials like this is g_x2top.
requires creation of a suitable .n2t file, the format for which is
described in
http://www.gromacs.org/Documentation/File_Formats/.n2t_File - the contents
should be fairly simple (one or two lines?) for silica.


> Another thing, I would like to assign different charge to different SI
> in my bulk. How can I achieve this?

...if you want to do this, there is no automated method.  You could, in
assign different residue names to each Si unit and assign that charge, but
the parameters of O are likely to be contingent upon the type of Si to
which it
is attached.  This eliminates g_x2top, which requires uniformity.  And as
above, this is not a task suited for pdb2gmx.  So either you need to (1) use
g_x2top and hack or (2) write your own sort of code/script to generate the


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