[gmx-users] Re: amount of solvent
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
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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