Your starting topology is already broken if you have a non-integral total
charge that's larger than the magnitude for floating point errors (in your
case, .02 is floating point error, the 0.55 is systematic). Try figuring
out where the charge assignments went wrong (the qtot column in the itp
Dear all :)
I have one extra question about Genion.
I want to neitralise my system with the qtot - 1.550002e by placing some Na
and Cl ions under the physiological concetrantion 100 mmol/l
I've performed
genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc
0.1 -neutral
bu
Dear James,
I was working for a longer time on ion placement within more or less
equilibrated structures. I found my nearly magical miracle solving those
problems in not using any gromacs tool for producing the input structure
but rather use the free software Packmol:
http://www.ime.unicamp.
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