[gmx-users] The energy minimization....
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Aug 16 10:27:28 CEST 2007
Hi,
Well, think harder about your 'problem'. How hard can it be to solve
all terms to reach the nearest local minimum for a system of 36 atoms?
You could basically do it by hand! No wonder that you reach
convergence to machine precision in 14 steps. Check the archives on
'stepsize too small' and 'convergence to machine precision', etc.
Cheers,
Tsjerk
On 8/16/07, mjduan at smail.hust.edu.cn <mjduan at smail.hust.edu.cn> wrote:
> http://www.gromacs.org/pipermail/gmx-users/2007-August/029155.html
>
>
>
> Mark:
> I am sorry to disturb you. I'm a beginner of GROMACS and this "mailing-list"
> system. I even don't know how to replay a post directly. And yesterday I
> haven't seen your replay because the list title changed, sorry again!
>
> About the problem, I haven't resolved it yet. The .top file of my ATP
> molecule is generated by the pdb2gmx, and the coordinates of each atom
> adopted to the pdb file. The force file is ffG43a2. Whether my topology file
> of ATP molecule have something wrong? The topology file of ATP as following:
>
> ; File '../ATP/ATP.top' was generated
> ; By user: root (0)
> ; On host: mjduan-desktop
> ; At date: Wed Aug 15 16:55:53 2007
> ;
> ; This is your topology file
> ; "Does All This Money Really Have To Go To Char ity ?" (Rick)
> ;
> ; Include forcefield parameters
> #include "ffG43a2.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> 1 NR 1 ATP AN9 1 -0.2 14.0067 ; qtot
> -0.2
> 2 C 1  60; ATP AC4 1 0.2 12.011
> ; qtot 0
> 3 NR 1 ATP AN3 2 -0.36 14.0067 ; qtot
> -0.36
> 4 CR1 1 ATP AC2 2 0.36 13.019 ; qtot
> 0
> 5 NR 1 ATP AN1 3 -0.36 14.0067 ; qtot
> -0.36
> 6 C 1 ATP AC6 3 0.36 12.011 ; qtot
> 0
> 7 NT 1 ATP AN6 4 -0.83 14.0067 ; qtot
> -0.83
> 8 H 1 ATP AH61 4 0.415 1.008 ; qtot
> -0.415
> 9 H 1&# 160; ATP AH62 4 0.415 1.008
> ; qtot 0
> 10 C 1 ATP AC5 5 0 12.011 ; qtot
> 0
> 11 NR 1 ATP AN7 5 -0.36 14.0067 ; qtot
> -0.36
> 12 CR1 1 ATP AC8 5 0.36 13.019&# 160;
> ; qtot 0
> 13 CH1 1 ATP AC1* 6 0.2 13.019 ; qtot
> 0.2
> 14 OA 1 ATP AO4* 6 -0.36 15.9994 ; qtot
> -0.16
> 15 CH1 1 ATP AC4* 6 0.16 13.019 ; qtot
> 0
> 16 CH1 1 ATP AC2* & #160; 7 0.15 13.019
> ; qtot 0.15
> 17 OA 1 ATP AO2* 7 -0.548 15.9994 ; qtot
> -0.398
> 18 H 1 ATP AH2* 7 0.398 1.008 ; qtot
> 0
> 19 CH1 1 ATP AC3* 8 0.15 13.019 ; qtot
> 0.15
> 20 &# 160; OA 1 ATP AO3* 8 -0.548 15.9994
> ; qtot -0.398
> 21 H 1 ATP AH3* 8 0.398 1.008 ; qtot
> 0
> 22 CH2 1 ATP AC5* 9 0 14.027 ; qtot
> 0
> 23 OA 1 ATP AO5* 10 -0.36  60; 15.9994
> ; qtot -0.36
> 24 P 1 ATP APA 10 0.705 30.9738 ; qtot
> 0.345
> 25 OM 1 ATP O1PA 10 -0.635 15.9994 ; qtot
> -0.29
> 26 OM 1 ATP O2PA 10 -0.635 15.9994 ; qtot
> -0.925
> 27 OA 1 ATP O3PA &# 160; 11 -0.36 15.9994
> ; qtot -1.285
> 28 P 1 ATP APB 11 0.705 30.9738 ; qtot
> -0.58
> 29 OM 1 ATP O1PB 11 -0.635 15.9994 ; qtot
> -1.215
> 30 OM 1 ATP O2PB 11 -0.635 15.9994 ; qtot
> -1.85
> 31 OA &# 160; 1 ATP O3PB 12 -0.36 15.9994
> ; qtot -2.21
> 32 P 1 ATP APG 12 0.63 30.9738 ; qtot
> -1.58
> 33 OM 1 ATP O1PG 12 -0.635 15.9994 ; qtot
> -2.215
> 34 OM 1 ATP O2PG 12 -0.635 15.9994 ; qtot
> -2.85
>   ; 35 OA 1 ATP O3PG 12 -0.548 15.9994
> ; qtot -3.398
> 36 H 1 ATP H3PG 12 0.398 1.008 ; qtot
> -3
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 2 gb_9
> 1   ; 12 2 gb_9
> 1 13 2 gb_21
> 2 3 2 gb_11
> 2 10 2 gb_15
> 3 4 2 gb_6
> 4 5 2 gb_6
> 5 6 2 gb_11
> 6 7 2 gb_8
> 6 10 2 gb_15
> 7 8 2 gb_2
> 7  ; 9 2 gb_2
> 10 11 2 gb_9
> 11 12 2 gb_9
> 13 14 2 gb_19
> 13 16 2 gb_25
> 14 15 2 gb_19
> 15 19 2 gb_25
> 15 22 2 gb_25
> 16 17 2 gb_19
> 16 19 2 gb_25
> 17 18 2 gb_1 19 20 2 gb_19
> 20 21 2 gb_1
> 22 23 2 gb_19
> 23 24 2 gb_27
> 24 25 2 gb_23
> 24 26 2 gb_23
> 24 27 2 gb_27
> 27 28 2 gb_27
> 28 29 2 gb_23
> 28 30 2 gb_23
> 28 31 2 0; gb_27
> 31 32 2 gb_27
> 32 33 2 gb_23
> 32 34 2 gb_23
> 32 35 2 gb_27
> 35 36 2 gb_1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 15 1
> 1 17 1
>  0; 1 19 1
> 2 14 1
> 2 16 1
> 5 8 1
> 5 9 1
> 7 11 1
> 8 10 1
> 9 10 1
> 12 14 1
> 12 16 1
> 13 18 1
> 13 20 1
> 13 22 1
> 14 17  0; 1
> 14 20 1
> 14 23 1
> 15 17 1
> 15 21 1
> 15 24 1
> 16 21 1
> 16 22 1
> 17 20 1
> 18 19 1
> 19 23 1
> 20 22 1
> 22 25 1
> 22 26 1
> 22 27 1
> 23 28 1
> 24 29 1
> 24 30 1
> 24 31 1
> 25 28 1
> 26 28 1
> 27 32 1
> 28 33 1
> 28 34 1
> 28 35 1
> 29 32 1
> 30 32 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 2 1 12 2 ga_6
> 2 1 13 2 ga_36
> 12 1 13 2 ga_36
> 1 2 3 2 ga_38
> 1 2 10 2 ga_6
> 3 2 10 2 ga_26
> 2 3 4 2 ga_26
> 3 4 5 2 ga_26
> 4 5 6 2 ga_26
> 5 6 7 2 ga_26
> 5 6 10 2 ga_26
> 7 6 10 2 ga_26
> 6 7 8 2 ga_22
> 6 7 9 2 ga_22
> 8 & #160; 7 9 2 ga_23
> 2 10 6 2 ga_26
> 2 10 11 2 ga_6
> 6 10 11 2 ga_38
> 10 11 12 2 ga_6
> 1 12 11 2 ga_6
> 1 13 14 2 ga_8
> 1 13 16 2 ga_8
> 14 13 16  0; 2 ga_8
> 13 14 15 2 ga_9
> 14 15 19 2 ga_8
> 14 15 22 2 ga_8
> 19 15 22 2 ga_7
> 13 16 17 2 ga_8
> 13 16 19 2 ga_7
> 17 16 19 2 ga_8
> 16 17 18 2 ga_11
> 15 19 16&# 160; 2 ga_7
> 15 19 20 2 ga_8
> 16 19 20 2 ga_8
> 19 20 21 2 ga_11
> 15 22 23 2 ga_8
> 22 23 24 2 ga_25
> 23 24 25 2 ga_13
> 23 24 26 2 ga_13
> 23 24 27 2 ga_4
> 25 24 26 2 ga_28
> 25 24 27 2 ga_13
> 26 24 27 2 ga_13
> 24 27 28 2 ga_25
> 27 28 29 2 ga_13
> 27 28 30 2 ga_13
> 27 28 31 2 ga_4
> 29 28 30 2 ga_28
> 29 28 31 2 ga_13
>  60; 30 28 31 2 ga_13
> 28 31 32 2 ga_25
> 31 32 33 2 ga_13
> 31 32 34 2 ga_13
> 31 32 35 2 ga_4
> 33 32 34 2 ga_28
> 33 32 35 2 ga_13
> 34 32 35 2 ga_13
> 32 35 36 2 ga_11
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 2 1 13 14 1 gd_6
> 10 6 7 8 1 gd_4
> 16 13 14 15 1 gd_14
> 1&# 160; 13 16 17 1 gd_7
> 14 13 16 17 1 gd_8
> 14 13 16 19 1 gd_17
> 14 13 16 19 1 gd_7
> 13 14 15 19 1 gd_14
> 14 15 19 16 1 gd_7
> 14 15 19 20 1 gd_8
> 22 15 19  0; 16 1 gd_17
> 22 15 19 20 1 gd_7
> 14 15 22 23 1 gd_8
> 19 15 22 23 1 gd_17
> 19 15 22 23 1 gd_7
> 13 16 17 18 1 gd_12
> 13 16 19 15 1 gd_17
> 13 16 19 20 1 gd_7
> 17 16 19 15 1 gd_7
> 17 16 19 20 1 gd_8
> 15 19 20 21 1 gd_12
> 15 22 23 24 1 gd_14
> 22 23 24 27 1 gd_11
> 22 23 24 27 1 gd_9
> 23 24 27 28 1 gd_11
> 23 24 27 28 1 gd_9
> 24 27 28 31 1 gd_11
> 24 27 28 31 1 gd_9
> 27 28 31 32 1 gd_11
> 27 28 31 32 1 gd_9
> 28 31 32 35 1 gd_11
> 28 31 32 35 1 gd_9
> 31 32 35 36 1 gd_11
> 31 32 35 36 1 gd_9
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3
> 1 12 11 10 2 gi_1
> 1 2 10 11 2 gi_1
> 1 12 2 13 2 gi_1
>  60; 2 3 4 5 2 gi_1
> 2 10 6 5 2 gi_1
> 2 1 3 10 2 gi_1
> 2 11 6 10 2 gi_1
> 2 1 12 11 2 gi_1
> 2 10 11 12 2 gi_1
> 3 2 10 6 2 gi_1
> 3 4 5 6 2 gi_1
> 4 3 2 10 2 gi_1
> 4 5 6 10 2 gi_1
> 6 9 8 7 2 gi_1
> 6 10 5 7 2 gi_1
> 10 2 1 12 2 gi_1
> 13 1 14   ; 16 2 gi_2
> 13 19 17 16 2 gi_2
> 15 14 22 19 2 gi_2
> 15 20 16 19 2 gi_2
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 & #160; 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> SOL 871
>
>
> --------------------------------
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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