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

[Justin A. Lemkul]

Andrew DeYoung wrote:
> Justin,
> 
> Thanks.  So I imagine that the order that the atoms are "stepped through" is
> dictated by the order of atoms in the configuration file (.gro or .pdb); do
> you think that this is correct?  I am not simulating a protein,  so other
> than the order of atoms in the configuration file, for my system there is
> not any obvious order to use (such as N terminus, H attached to N terminus,
> C-alpha, etc).
> 

Yes, from everything I can tell the order that is used is the one found in the 
coordinate file.

-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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