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

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 22 19:30:57 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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