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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 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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