[gmx-users] Creating an atomtype where all nonbonded interactions are enumerated

[Justin A. Lemkul]

Andrew DeYoung wrote:
> Hi,
> 
> I am trying to simulate a liquid (EMI-BF4) in a box with two walls, one at
> z=0 and one at z=z_0.  I am trying to create a new atom type to use as my
> walls' atom type, so that I can manipulate the interaction between the atoms
> of the liquid and the atoms of the wall.  I am basing this idea on the
> manual (http://manual.gromacs.org/current/online/mdp_opt.html#walls), which
> in the walls section describes how wall_atomtype can be used:
> 
> "wall_atomtype: the atom type name in the force field for each wall. By (for
> example) defining a special wall atom type in the topology with its own
> combination rules, this allows for independent tuning of the interaction of
> each atomtype with the walls."
> 
> In my force field, atoms within the liquid interact with each other by
> combination rule 3, which means that in ffnonbonded.itp, I specify sigma and
> epsilon for each atom type in my liquid.  This is specified in my main
> topology (mytopology.top), which includes a statement #include
> "./forcefield.itp".  forcefield.itp, in turn, contains the following: 
> 
> ---
> ; forcefield.itp
> #define _FF_GRAPHENE_EMI
> 
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 	1              3               yes             0.5     0.5
> 
> #include "./ffnonbonded.itp"
> #include "./ffbonded.itp"
> ---
> 
> But what if I now want to define a new atom type (called mywall) that will
> interact with the liquid, but not in the standard way (i.e., not by
> specifying sigma and epsilon and using combination rule 3 to handle cross
> terms)?  I would like to enumerate all of the possible sigma_ij's and
> epsilon_ij's, where i is "mywall" and j is an atom type from the liquid.
> 
> So, I wrote a new file called mywall.itp:
> 
> ---
> ; mywall.itp
> [ moleculetype ]
> ; name nrexcl
> mywall 3
> 
> [ nonbond_params ]
> ; i j func sig eps
> mywall N 1 0.29750 4.56912
> mywall C 1 0.31200 3.07524
> mywall H 1 0.26170 1.17675
> mywall B 1 0.31225 3.48667
> mywall F 1 0.28974 2.82420
> ---
> 
> where I have specified all of the sigma_ij's and epsilon_ij's.  I try to
> include this file by using the following mytopology.top:
> 
> ---
> ; mytopology.top
> #include "./forcefield.itp"
> #include "./emi_flex.itp"
> #include "./bf4.itp"
> #include "./mywall.itp"
> 
> [ system ]
> IL
> 
> [ molecules ]
> ; Name number
> EMI  256
> BF4  256
> ---
> 
> When I use these files and run grompp, I get this error message:
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: toppush.c, line: 1166
> 
> Fatal error:
> Atomtype mywall not found
> -------------------------------------------------------
> 
> One problem I see with what I have done is that in mywall.itp, I am defining
> a moleculetype "mywall", whereas I really want to define an atomtype
> "mywall".  However, I am not exactly sure how to do this.  Normally, I would
> define an atomtype in ffnonbonded.itp in my homemade force field, with a
> line like this (for boron, for example):
> 
> [ atomtypes ]
> ;type at.n	mass   charge   ptype  sig   eps
>   B   5   10.81000   1.1504   A   3.58140e-1    3.97480e-1
> 
> But I don't want to just specify (single values of) sigma and epsilon.
> Rather, I want to enumerate all of the sigma_ij's and epsilon_ij's, using
> perhaps a "[ nonbond_params ]"-like directive.  Can you please help me know
> how to do this?
> 

See the Gromos force fields for an example, since they operate this way.  LJ 
nonbonded interactions are generated using sigma and epsilon unless a special 
set of parameters is specified in [nonbond_params].

-Justin

-- 
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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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