[gmx-users] How to fix the position of Au in my MD.
Yongqiang Wang
ywang525 at uwo.ca
Fri Jul 28 15:40:15 CEST 2006
I am a new user of Gromacs and am conducting a MD simulation of
SAM(self-assembled-monolayer) in gold(111) surface.
Here is my .itp .top and .mdp file during energy minimization. I want to fix
the position of gold atoms, but in simulation the gold atoms run around.
Who can help me? Thank you so much.
******TAL.itp************
[ moleculetype ]
; molname nrexcl
TAL 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 F 1 TAL FA 1 -0.20
2 F 1 TAL FB 1 -0.20
3 F 1 TAL FC 1 -0.20
4 C 1 TAL CT 1 0.54
5 C 1 TAL CB 2 -0.30
6 H 1 TAL HB1 2 0.25
7 H 1 TAL HB2 2 0.25
8 S 1 TAL S 3 -0.50
9 Au 2 TAL Au1 4 0.12
10 Au 2 TAL Au2 4 0.12
11 Au 2 TAL Au3 4 0.12
[ bonds ]
; i j funct length force.c.
4 1 1 1.370000e-01 4.184000e+05
4 2 1 1.370000e-01 4.184000e+05
4 3 1 1.370000e-01 4.184000e+05
4 5 1 1.530000e-01 3.347000e+05
5 6 1 0.109 345000
5 7 1 0.109 345000
5 8 1 0.184 345000
9 8 1 0.2465 185769
10 8 1 0.2475 185769
11 8 1 0.2585 185769
[ angles ]
; i j k funct angle force.c.
1 4 2 1 1.076000e+02 4.602000e+02
1 4 3 1 1.076000e+02 4.602000e+02
2 4 3 1 1.076000e+02 4.602000e+02
1 4 5 1 111.80 383
2 4 5 1 111.80 383
3 4 5 1 111.80 383
6 5 7 1 109.47 383
6 5 4 1 108.27 383
7 5 4 1 108.27 383
8 5 4 1 113.00 383
8 5 6 1 109.00 383
8 5 7 1 109.00 383
9 8 5 1 132.60 383
10 8 5 1 121.40 383
11 8 5 1 145.60 383
9 8 10 1 79.00 383
10 8 11 1 74.70 383
11 8 9 1 77.35 383
[ dihedrals ]
; ai aj ak al funct phai0 k n
8 5 4 1 1 1.80000e+02 3.347200e+01 3
8 5 4 2 1 -0.61500e+02 3.347200e+01 3
8 5 4 3 1 0.61500e+02 3.347200e+01 3
9 8 5 4 1 -125.6 3.347200e+01 1
10 8 5 4 1 129.35 3.347200e+01 1
11 8 5 4 1 19.2 3.347200e+01 1
#ifdef POSRES
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
11 1 1000 1000 1000
#else
[ position_restraints ]
; i funct fcx fcy fcz
9 1 1000 1000 1000
10 1 1000 1000 1000
11 1 1000 1000 1000
#endif
*******SUB.itp************
[ moleculetype ]
; molname nrexcl
SUB 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifdef _FF_GROMACS
1 Au 1 SUB Aub 1 0.0
#endif
#ifdef _FF_GROMOS96
1 Au 1 SUB Aub 1 0.0 196.9665
#endif
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
*********.top**********
; Include forcefield parameters
#include "ffgmx.itp"
#include "gold.itp"
; Include water topology and thiol toppology.
#include "TAL.itp"
#include "SUB.itp"
#incluse "spc.itp"
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
thiol_au_thl in water
[ molecules ]
; Compound #mols
TAL 28
SUB 504
SOL 746
*********em.mdp************
title = Thiolau Energy Minimization
cpp = /usr/bin/cpp
define = -DFLEX_SPC -DPOSRES
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 400
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.01
_EOF_
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