[gmx-users] How to get one T coupling for a multi component systems ?

[Tandia, Adama]

Dear All:
I want to run a MD of a structure composed of thousands of atoms belonging to n (n>> 2) different types.
There is no bonding between atoms of the system.
I developed the following .top file, which required n different T couplings

%%%%%%%%%%%%%%%%%%%

[ moleculetype ]
; name nrexcl
SiG	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1       SiG    	1     	SiG	SiG     1       4.0     128.08000

[ moleculetype ]
; name nrexcl
B	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Be	1	B	B	1	3.0	10.81

[ moleculetype ]
; name nrexcl
O	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	O	1	O	O	1	-2.0	16.00

[ moleculetype ]
; name nrexcl
Na	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Na	1	Na	Na	1	1.0	22.99

[ moleculetype ]
; name nrexcl
Mg	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Mg	1	Mg	Mg	1	2.0	24.31

[ moleculetype ]
; name nrexcl
Al	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Al	1	Al	Al	1	3.0	26.98

[ moleculetype ]
; name nrexcl
As	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	As	1	As	As	1	3.0	74.91

[ moleculetype ]
; name nrexcl
Sr	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Sr	1	Sr	Sr	1	2.0	87.62

[ moleculetype ]
; name nrexcl
Ba	0
[ atoms ]
; nr   type   resnr  residue   atom   cgnr   charge      mass
1	Ba	1	Ba	Ba	1	2.0	137.33
...

[ system ]
GLASS_SYSTEM

[ molecules ]
SiG	
O	
B
Mg
Ba
...

%%%%%%%%%%%%%%%%%%%

A first guess, probably wrong, would be to consider the whole system as one molecule and gothe folowing way:
[ moleculetype ]
; name	nrexcl
GLASS	0
[ atoms ]
1     SiG   1     GLASS	SiG   1     4.0   28.08000
2	B	1	GLASS	B	1	3.0	10.81
3	O	1	GLASS	O	1	-2.0	16.00
4	Na	1	GLASS	Na	1	1.0	22.99
5	Mg	1	GLASS	Mg	1	2.0	24.31
6	Al	1	GLASS	Al	1	3.0	26.98
7	Ca	1	GLASS	Ca	1	2.0	40.08
8	As	1	GLASS	As	1	3.0	74.91
9	Sr	1	GLASS	Sr	1	2.0	87.62
10	Ba	1	GLASS	Ba	1	2.0	137.33

[ system ]
GLASS_SYSTEM

[ molecules ]
GLASS 2004
 I'm afraid that this will consider the system as composed of 2004 molecules, with a total number of atoms of 10*2004=20040!

Any help?

Adama Tandia
Modeling & Simulation
Corning INC
Corning, NY 14831 USA
Tel:  607 248 1036
Fax: 607 974 3405
www.corning.com <www.corning.com> 

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