[gmx-users] rerun under non-bonded E. terms

Albert Solernou a.solernou at leeds.ac.uk
Tue May 12 12:59:01 CEST 2015

I am getting fairly large values for the LJ energy term (order 10^8), 
while previous values were much better (order 10^5). I am wondering 
whether there is a radius decrease for bonded atoms or something 
equivalent to explain these differences. I browsed quickly the manual 
but could not find any clear explanation.

Any ideas?


On 05/08/2015 03:48 PM, Albert Solernou wrote:
> Thanks for being so quick.
> Cheers,
> Albert
> On 05/08/2015 03:44 PM, Justin Lemkul wrote:
>> On 5/8/15 10:43 AM, Albert Solernou wrote:
>>> Thanks Justin,
>>> by removing all the bonded terms from the topology you mean edit
>>> "topol_Protein_chain_A.itp"  and remove the sections "bonds", "pairs", "angles",
>>> and "dihedrals"?
>> Yes, but of course this renders the topology nonfunctional, so make sure you
>> keep a backup.  This applies to any and all topologies that have any bonded
>> terms in them.
>> -Justin

   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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