[gmx-users] Break down of total energy
Moeed
lecielll at googlemail.com
Fri May 21 20:50:14 CEST 2010
Hello Justin,
As for exclusions, in the manual I see 1-4 interactions refer to carbon
atoms on the backbone. I do not know if it makes sense if I enter a number
more than 5 (hexane has only 6 carbons), However, I did so and I changed
nrexcl from default value of 3 to 19 ( to exlude all interactions between
all C and H atoms!) but I got the following message after grompp em step:
checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 19 bonded neighbours molecule type 'Hexane'
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: smalloc.c, line: 147
Fatal error:
Not enough memory. Failed to calloc 78089438 elements of size 8 for s
(called from file topexcl.c, line 161)
-------------------------------------------------------
I also tried another approach (although I am almost sure this is not the
proper way of excluding ALL interactions as in this way I think I am
excluding atom 1 and all other atoms only!) and added exclusions directive
as you see below in top file
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Hexane 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 HEX C1 1 -0.18 12.011 ; qtot
-0.18
2 opls_140 1 HEX H11 1 0.06 1.008 ; qtot
-0.12
3 opls_140 1 HEX H12 1 0.06 1.008 ; qtot
-0.06
4 opls_140 1 HEX H13 1 0.06 1.008 ; qtot
0
5 opls_158 1 HEX C2 2 -0.12 12.011 ; qtot
-0.12
6 opls_140 1 HEX H21 2 0.06 1.008 ; qtot
-0.06
7 opls_140 1 HEX H22 2 0.06 1.008 ; qtot
0
8 opls_158 1 HEX C3 3 -0.12 12.011 ; qtot
-0.12
9 opls_140 1 HEX H31 3 0.06 1.008 ; qtot
-0.06
10 opls_140 1 HEX H32 3 0.06 1.008 ; qtot
0
11 opls_158 1 HEX C4 4 -0.12 12.011 ; qtot
-0.12
12 opls_140 1 HEX H41 4 0.06 1.008 ; qtot
-0.06
13 opls_140 1 HEX H42 4 0.06 1.008 ; qtot
0
14 opls_158 1 HEX C5 5 -0.12 12.011 ; qtot
-0.12
15 opls_140 1 HEX H51 5 0.06 1.008 ; qtot
-0.06
16 opls_140 1 HEX H52 5 0.06 1.008 ; qtot
0
17 opls_157 1 HEX C6 6 -0.18 12.011 ; qtot
-0.18
18 opls_140 1 HEX H61 6 0.06 1.008 ; qtot
-0.12
19 opls_140 1 HEX H62 6 0.06 1.008 ; qtot
-0.06
20 opls_140 1 HEX H63 6 0.06 1.008 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 8 1
8 9 1
8 10 1
8 11 1
11 12 1
11 13 1
11 14 1
14 15 1
14 16 1
14 17 1
17 18 1
17 19 1
17 20 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 9 1
1 10 1
1 11 1
2 6 1
2 7 1
2 8 1
3 6 1
3 7 1
3 8 1
4 6 1
4 7 1
4 8 1
5 12 1
5 13 1
5 14 1
6 9 1
6 10 1
6 11 1
7 9 1
7 10 1
7 11 1
8 15 1
8 16 1
8 17 1
9 12 1
9 13 1
9 14 1
10 12 1
10 13 1
10 14 1
11 18 1
11 19 1
11 20 1
12 15 1
12 16 1
12 17 1
13 15 1
13 16 1
13 17 1
15 18 1
15 19 1
15 20 1
16 18 1
16 19 1
16 20 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 1
2 1 4 1
2 1 5 1
3 1 4 1
3 1 5 1
4 1 5 1
1 5 6 1
1 5 7 1
1 5 8 1
6 5 7 1
6 5 8 1
7 5 8 1
5 8 9 1
5 8 10 1
5 8 11 1
9 8 10 1
9 8 11 1
10 8 11 1
8 11 12 1
8 11 13 1
8 11 14 1
12 11 13 1
12 11 14 1
13 11 14 1
11 14 15 1
11 14 16 1
11 14 17 1
15 14 16 1
15 14 17 1
16 14 17 1
14 17 18 1
14 17 19 1
14 17 20 1
18 17 19 1
18 17 20 1
19 17 20 1
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 5 6 3
2 1 5 7 3
2 1 5 8 3
3 1 5 6 3
3 1 5 7 3
3 1 5 8 3
4 1 5 6 3
4 1 5 7 3
4 1 5 8 3
1 5 8 9 3
1 5 8 10 3
1 5 8 11 3
6 5 8 9 3
6 5 8 10 3
6 5 8 11 3
7 5 8 9 3
7 5 8 10 3
7 5 8 11 3
5 8 11 12 3
5 8 11 13 3
5 8 11 14 3
9 8 11 12 3
9 8 11 13 3
9 8 11 14 3
10 8 11 12 3
10 8 11 13 3
10 8 11 14 3
8 11 14 15 3
8 11 14 16 3
8 11 14 17 3
12 11 14 15 3
12 11 14 16 3
12 11 14 17 3
13 11 14 15 3
13 11 14 16 3
13 11 14 17 3
11 14 17 18 3
11 14 17 19 3
11 14 17 20 3
15 14 17 18 3
15 14 17 19 3
15 14 17 20 3
16 14 17 18 3
16 14 17 19 3
16 14 17 20 3
; 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 1000 1000
;#endif
; Include generic topology for ions
;#include "ions.itp"
*[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
*
[ system ]
; Name
Hexane
[ molecules ]
; Compound #mols
Hexane 125
*************************************************
Then I used the following comamnds:
grompp -f em -c Hexane-Stack125.gro -p Hexane-Stack125-nrexcl19.top -o
Hexane-Stack125_em >& output.grompp_em
mdrun -s Hexane-Stack125_em -o Hexane-Stack125_em -c Hexane-Stack125_b4pr -v
>& output.mdrun_em
grompp -f md13 -c Hexane-Stack125_b4pr -p Hexane-Stack125-nrexcl19.top -o
Hexane-Stack125_md >& output.grompp_md
mdrun -rerun Hexane-Stack125_md.tpr.trr
-------------------------------------------------------
Program mdrun, VERSION 4.0.7
Source code file: gmxfio.c, line: 737
Can not open file:
topol.tpr
**********************************************************************************************
Do I need to do this as:
[exclusions]
1 2
1 3
1 4
...
1 20
2 3
3 4
.
.
3 20
.
.
since this involves tedious work I would like you to help me with first
approach (nrexcl in moleculetype) and let me know what wrong is..
Thank you,
moeed
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