[gmx-users] Re: amount of solvent

Christopher Neale chris.neale at mail.utoronto.ca
Tue Oct 16 04:25:34 CEST 2012

Not answering your main question here, just pointing out that you should try:

trjconv -pbc mol -ur compact

and then visualize with VMD to see if you are actually getting what you want after all.


-- original message --

I already pack the mixed solvent by using packmol cause the box that i
used octahedron.Therefore the error that coming out is that topology
and the gro file does not
same. When I view the solvent by VMD  its just shows that the mixture
only fill in the cubic form even though the starting box that i need
was octahedron.
So I would like to ask you guys if I already pack all the molecule,i
need to create the new topology right? before start to minimize?


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