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

[Justin A. Lemkul]

Andrew DeYoung wrote:
> Justin,
> 
> Thank you so much for your help!  That was really helpful.
> 
> It seems that I simply append my [ nonbond_params ] section to the end of my
> ffnonbonded.itp file.  However, if I ONLY have this:
> 
> ---
> ; ffnonbonded.itp
> [ atomtypes ]
> ;type at.n	mass	charge  ptype  sig  eps
> ; all of the liquid atomtypes
> ; ...
> 
> [ 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
> ---
> 
> then I get an error message saying that atomtype mywall does not exist.
> However, if I simply add a bogus entry for mywall in the [ atomtypes ]
> section of ffnonbonded.itp, then grompp runs fine:
> 

Right, you can't use an atomtype unless it is defined.

> ---
> ; ffnonbonded.itp
> [ atomtypes ]
> ;type at.n	mass	charge  ptype  sig  eps
> mywall 6  12.01100  0.000 A 0.00000e-1 0.00000e-1 ; bogus sig and eps
> ; all of the liquid atomtypes
> ; ...
> 
> [ 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
> ---
> 
> Is there any way that I can verify that the code is actually using the
> parameters for mywall in the [ nonbond_params ] section, rather than the
> bogus parameters (0 for sig and eps) for mywall in the [ atomtypes ]
> section?
> 

Run gmxdump on your .tpr file.  All the relevant parameters should be in there 
somewhere.

-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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