[gmx-users] setting up forcefield
saicheong chung
saicheong.chung at jp.sony.com
Fri Dec 21 03:51:21 CET 2001
Dear all,
I tried to run a simulation of the polymer with
SHAKE-fixed bond/angles. Taking into account
only the dihedrals, charge and LJ forces. I
want to use a non-default forcefield taking from
a publication.
I somehow managed to take the trouble of mimicing the
ffgmx forcefield and created the corresponding files
in the "top" directory. And pdb2gmx and grompp are
able to generate the tpr file. However, there must
be something wrong that my molecule is alway exploding
and got the "shake error". I am at lost where to
look now. Would you please give me some tips?
attached are the forcefield files and the test.
thanks
sai
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CF 12.01100 ; flurinated carbon (C-F)
SO 32.066 ; sulphite S (SO3-)
OS 15.99940 ; oxygen in sulphite (SO3-)
FC 18.99840 ; fluorine bonded to carbon (C-F)
O1 15.99940 ; ether oxygen in nafion side chain
CH3 15.0350 ; CH3
OW 15.99940 ; WATER OXYGEN
HW 1.00800 ; WATER HYDROGEN
KP 39.0983 ; potassium ion
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; Residual files for the simulation of nafion related materials
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 1 2
[ NAF ]
[ atoms ]
CH3 CH3 0.000 0
C1 CF 0.329 0
F11 FC -0.166 0
F12 FC -0.166 0
C2 CF 0.329 0
F21 FC -0.166 0
F22 FC -0.166 0
O1 O1 -0.260 0
C3 CF 0.322 0
F31 FC -0.166 0
F32 FC -0.166 0
C4 CF 0.322 0
F41 FC -0.328 0
F42 FC -0.328 0
S1 SO 1.412 0
O12 OS -0.632 0
O13 OS -0.632 0
O11 OS -0.632 0
K KP +1.000 1
[ bonds ]
CH3 C1
C1 F11
C1 F12
C1 C2
C2 F21
C2 F22
C2 O1
O1 C3
C3 F31
C3 F32
C3 C4
C4 F41
C4 F42
C4 S1
S1 O12
S1 O13
S1 O11
[ dihedrals ]
; ai aj ak al funct c0 c1
CH3 C1 C2 O1
C1 C2 O1 C3
C2 O1 C3 C4
O1 C3 C4 S1
C3 C4 S1 O
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[ atomtypes ]
;name mass charge ptype c6 c12
CF 12.01100 0.000 A 2.79435e-03 4.90354e-06
SO 32.066 0.000 A 8.37856e-03 1.67702e-05
OS 15.99940 0.000 A 3.27154e-03 3.19607e-06
FC 18.99840 0.000 A 1.06291e-03 9.30631e-07
O1 15.99940 0.000 A 2.38335e-03 1.99534e-06
CH3 15.03500 0.000 A 0.88765E-02 0.26150E-04
#ifdef HEAVY_H
OW 9.95140 0.000 A 0.26171E-02 0.26331E-05
#else
OW 15.99940 0.000 A 0.26171E-02 0.26331E-05
#endif
#ifdef HEAVY_H
HW 4.03200 0.000 A 0.00000E+00 0.00000E+00
#else
HW 1.00800 0.000 A 0.00000E+00 0.00000E+00
#endif
KP 39.0983 0.000 A 0.88765E-02 0.26150E-04
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;
; File 'topol.top' was generated
; By user: taro (39586)
; On host: SGI-ryuichiro
; At date: Sat Apr 21 20:28:39 2001
;
; This is your topology file
; "In a Deep Deep Well" (Nick Cave)
;
; Include forcefield parameters
#include "ffnafi.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 CH3 1 NAF CH3 1 0 15.035 ; qtot 0
2 CF 1 NAF C1 1 0.329 12.011 ; qtot 0.329
3 FC 1 NAF F11 1 -0.166 18.9984 ; qtot 0.163
4 FC 1 NAF F12 1 -0.166 18.9984 ; qtot -0.00299999
5 CF 1 NAF C2 1 0.329 12.011 ; qtot 0.326
6 FC 1 NAF F21 1 -0.166 18.9984 ; qtot 0.16
7 FC 1 NAF F22 1 -0.166 18.9984 ; qtot -0.00599998
8 O1 1 NAF O1 1 -0.26 15.9994 ; qtot -0.266
9 CF 1 NAF C3 1 0.322 12.011 ; qtot 0.056
10 FC 1 NAF F31 1 -0.166 18.9984 ; qtot -0.11
11 FC 1 NAF F32 1 -0.166 18.9984 ; qtot -0.276
12 CF 1 NAF C4 1 0.322 12.011 ; qtot 0.046
13 FC 1 NAF F41 1 -0.328 18.9984 ; qtot -0.282
14 FC 1 NAF F42 1 -0.328 18.9984 ; qtot -0.61
15 SO 1 NAF S1 1 1.412 32.066 ; qtot 0.802
16 OS 1 NAF O12 1 -0.632 15.9994 ; qtot 0.17
17 OS 1 NAF O13 1 -0.632 15.9994 ; qtot -0.462
18 OS 1 NAF O11 1 -0.632 15.9994 ; qtot -1.094
19 KP 1 NAF K 2 1 39.0983 ; qtot -0.0940001
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
2 3 1
2 4 1
2 5 1
5 6 1
5 7 1
5 8 1
8 9 1
9 10 1
9 11 1
9 12 1
12 13 1
12 14 1
12 15 1
15 16 1
15 17 1
15 18 1
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 5 8 1
2 5 8 9 1
5 8 9 12 1
8 9 12 15 1
9 12 15 16 1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
SOL 121
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GRowing Old MAkes el Chrono Sweat
19
1NAF CH3 1 0.906 0.529 0.720
1NAF C1 2 0.894 0.667 0.641
1NAF F11 3 0.822 0.648 0.525
1NAF F12 4 1.018 0.713 0.608
1NAF C2 5 0.814 0.774 0.730
1NAF F21 6 0.887 0.804 0.842
1NAF F22 7 0.694 0.721 0.769
1NAF O1 8 0.789 0.887 0.656
1NAF C3 9 0.753 0.991 0.740
1NAF F31 10 0.665 0.947 0.836
1NAF F32 11 0.866 1.038 0.802
1NAF C4 12 0.685 1.108 0.655
1NAF F41 13 0.576 1.054 0.591
1NAF F42 14 0.775 1.147 0.559
1NAF S1 15 0.636 1.248 0.757
1NAF O12 16 0.637 1.368 0.668
1NAF O13 17 0.746 1.246 0.858
1NAF O11 18 0.502 1.208 0.808
1NAF K 19 0.741 1.485 0.971
1.51600 1.95600 1.44600
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