[gmx-users] 1-4 interaction at distance larger than 1

[Michael Brunsteiner]

--- Makoto Yoneya <yoneya at nanolc.jst.go.jp> wrote:
> Dear GROMOS users:
> 
> I'm having start-up MD of my system.
> My system (with 256 identical molecules) looks reasonably energy
> minimized
> (the minimized coordinates looks no problem).
> However, in the successive start up dynamics run, I'd receive the
> following
> warnings
> and the job aborted even with low density without any close molecular
> pairs.
> 
> "Warning: 1-4 interaction at distance larger than 1"

if you added a self-made topology in an rtp file then the problem 
could be that pdb2gmx makes bonds between atoms in different
molecules ... you might want to check the bonds in the 
generated top files

> and with -debug, I found many lines like,
> 
> 1-4 (13056,13044) interaction not within cut-off! r=610401.
> Ignored760.327227 -1139.533479 5745.167765
> 6203.901758 -22150.204428 114820.642023
> 
> What can be tried to find out the cause of these behaviors, and avoid
> it.
> Please give me a hint for it.
> 
> Best regards.
> 
> Makoto Yoneya, Dr.
> Yokoyama Nano-LC Project
> Tsukuba, Japan
> 
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