[gmx-users] Distance restrain with dummy atom

anu chandra anu80125 at gmail.com
Tue Aug 11 14:30:57 CEST 2015

Dear Gromacs users,

I am working with membrane simulations and I would like to put distance
restrain along Z-axis between a dummy atom I generated at the centre of box
and all the water molecules. For this, I first generated a dummy atom at
the centre of box and also made a simple .itp file for it as shown below,

[ moleculetype ]
; molname   nrexcl
DUM     1

[ atoms ]
; id    at type     res nr  residu name at name  cg nr  charge
1   MW      1   DUM     DUM  0  0  1

I am using charmm36 ff and atom type MW is special dummy particle mention
in the charmm36 ffnonbonded.itp file, as shown below.

; special dummy-type particles
MNH3    0   0.000000    0.00    A   0.0 0.0
MNH2    0   0.000000    0.00    A   0.0 0.0
MCH3    0   0.000000    0.00    A   0.0 0.0
MCH3S   0   0.000000    0.00    A   0.0 0.0
*MW *
* 0   0.000000    0.00    A   0.0 0.0*
Am I doing it correct here, for generating a dummy atom? Am I doing correct
with provide hydrogen mass to dummy atom?

Few other queries regarding the distance restrain are,

1. How do I make sure that the dummy atom do not fly away from the centre
of box?

2. What steps I should take to generate a file for distance restrain
between dummy atom and water molecules?

Please help me to clarify these queries. Waiting for your valuable reply.

Many thanks in advance

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