Hello Justin,<br><br>Thanks for your comments. Actually, since I am interested in only interaction energies <b>between</b> molecules I thought by excluding energies between atoms on a single chain what I get from nonbonded interactions would not include 1-4 interactions. <br>
<br>*********************************************<br>This is from previous posts:<br><br>Question: Can I not take for<br>
instance LJ energy values which are coming from a specific NO. of molecuels<br>
in simulation box and calculate interaction energies for pairs or "mol"<br>
number of molecules?<br><br>Your answer:<br><br>Not easily. You will still have intramolecular terms that are not covered by<br>
the 1-4 interactions. <b>For example, if the two ends of your molecule interact<br>
with one another, this interaction will contribute to your nonbonded energies.</b><br>*********************************************************************************************<br>That is why I thought I have to exclude interaction in a single chain between atoms, so that for instance atoms 1 and 20 do not see each other.<br>
<br>I manual I found only about how extra exlusion within a molecue cab added in [exclusions].. I dont think this helps me.<br><br>How can I define all possible intramolecular exclusions in order to save only intermolecular energy contributions?<br>
<br><br>top file:<br>
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<p style="margin-bottom: 0cm;"> Include forcefield parameters</p>
<pre>#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Hexane 3
[ exclusions ]
??<br>
[ 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"
[ system ]
; Name
Hexane
[ molecules ]
; Compound #mols
Hexane 125</pre>
<br><br>Thank you,<br><br><br>
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