[gmx-users] no domain decomposition

[soumadwip ghosh]

Hi Mark and Justin,
           actually I have simulated each item with pure SPCE water
separately for a few nanoseconds and they are absolutely fine. The
initial structure ( a small dna inside a CNT) was generated using
Packmol and may be due to this I have this error occuring each time.
Justin asked me to carefully look into the nvt.log file which I have
attached in my previous mail. But I am unable to detect any source of
that error from it. Tsjerk suggested that for my system -nt has to be
kept less than 8. I tried that too but the same LINCS warning pops up.
My question is is there any way to fix the problem using some options
in the mdrun prompt? I  think I have correct topologies since I am
able to simulate each species separately. Hence, technically is there
a viable solution? Like I can tell you I deliberately kept the box
size 1000 nm3 to replicate some observations while the use of editconf
sugeested the box size should be 580 nm3 but can this be the issue? At
this point I am thinking of repeating the simulation keeping a small
box in mind. However, it would be really helpful if someone can
provide some insights in fixing this problem .

Regards,
Soumadwip