[gmx-users] breaking down total energy
Justin A. Lemkul
jalemkul at vt.edu
Thu May 20 13:36:49 CEST 2010
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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