[gmx-users] Distance restrain with dummy atom
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
[ 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
* 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
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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