Alif M Latif wrote:
Dear GROMACS users and developers,
I've done 1 ns
simulation before this, and the water seems to remain in the micelle
structure. I'm using a single workstation with Pentium D, 3.0 GHz, and
2Gb of RAM, so I can't manage to get 0.5-1 ns per day.
Yeah, a nanosecond is nothing :-O
About the vdwradii.dat that you all said, I'll try to do it. But i'm a
beginner in this field (I'm a chemist)..It will take time. By the way, I
just thought using Packmol to initially arrange the water to be outside
the sphere. So I don't have to use genbox. Can I do that?
Don't know... please consult the packmol documentation :-) It's
off-topic here. So long as the structure file you give to pdb2gmx uses
residue names it can recognise as water, you should be OK.
Mark
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