On 2013-06-07 04:12, Justin Lemkul wrote:
On 6/6/13 10:00 PM, Badamkhatan wrote:
Dear GMX-users
Recently i got this error and note from my MD2 simulation. I'm solvating
1-octanol to 1-octanol and calculating free energy differences. This
is the
last step of my calculation and previous steps are looking fine.
Basically i
followed Justin's free energy tutorial.
Here is
Note:
A list of missing interactions:
LJC Pairs NB of 210 missing 1
exclusions of 25308 missing 1
Molecule type '1-octanol'
the first 10 missing interactions, except for exclusions:
LJC Pairs NB atoms 3 25 global 3 25
Fatal error:
2 of the 57736 bonded interactions could not be calculated because some
atoms involved moved further apart than the multi-body cut-off
distance (1
nm) or the two-body cut-off distance (1 nm), see option -rdd, for
pairs and
tabulated bonds also see option -ddcheck
Please help me and suggest any idea to solve this problem?
Sounds like you're
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
It may also be the opposite, box shrinking under equilibration.
Try:
mdrun [options] -rdd 1.25
-Justin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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