Moeed wrote:
Hello Justin,
Thanks for your comments. Actually, since I am interested in only
interaction energies *between* molecules I thought by excluding energies
between atoms on a single chain what I get from nonbonded interactions
would not include 1-4 interactions.
OK, I see what you're doing, your approach was just wrong. The simplest thing
to do is the following. First, run a normal MD simulation, no fancy exclusions
or anything, until you have produced a stable hexane system that reproduces
whatever observable quantities you have decided upon. Know what you're looking
for first!
Then, modify the topology to add the exclusions you want. It is a whole lot
easier to simply increase the number given in nrexcl within the [moleculetype]
definition to take care of all possible interactions than anything else.
There's nothing wrong with doing it manually (somewhere *after* the atoms have
been defined, but before the end of the [moleculetype] definition), it's just
more work.
There is no need for special energygrps or energygrp_excl for your purpose,
since those exclusions are applied to intermolecular interactions, not
intramolecular interactions, and they are not dependent upon [exclusions]
defined in the topology.
Once you have a suitably modified topology, use mdrun -rerun on the original
trajectory.
-Justin
*********************************************
This is from previous posts:
Question: Can I not take for
instance LJ energy values which are coming from a specific NO. of molecuels
in simulation box and calculate interaction energies for pairs or "mol"
number of molecules?
Your answer:
Not easily. You will still have intramolecular terms that are not
covered by
the 1-4 interactions. *For example, if the two ends of your molecule
interact
with one another, this interaction will contribute to your nonbonded
energies.*
*********************************************************************************************
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.
I manual I found only about how extra exlusion within a molecue cab
added in [exclusions].. I dont think this helps me.
How can I define all possible intramolecular exclusions in order to save
only intermolecular energy contributions?
top file:
Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Hexane 3
[ exclusions ]
??
[ 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
Thank you,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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