TJ Mustard wrote:
Hi all,
We have been running a lot of simulations on protein ligand
interactions, and my settings/setup/mdp files worked great for one
system. Then when we moved to a larger and more complicated system we
started getting mdrun 1-4 interaction errors in our MD.
We are running with heavyh and have correctly made our ligands with
acpype and edited to have heavyh.
Same setup as our smaller simpler model, but keep getting these:
Warning: 1-4 interaction between X and Y at distance 1.804 which is
larger than 1-4 table size 1.800 nm.
The jobs will continue on and finish but we are worried about the error
that could be included with these errors.
Is this related to the other issue we're discussing? If so, please do not
double-post, especially if you're including different information in different
threads. It becomes a nightmare to try to keep track of.
That particular error is usually not a good sign. Normal, stable simulations
should not give such an error.
-Justin
Any help would be appreciated. Also I can attach my mdp files.
Thank you,
TJ Mustard
Email: [email protected]
--
========================================
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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