[gmx-users] Vacuum simulation in GMX 5
fileti at gmail.com
Thu May 7 14:43:36 CEST 2015
Justin, thanks for the help.
Originally I have tried the options you suggested, and the GMX 5 not
accepted well, since there are not more -pd option, which allowed to
perform the calculation with pbc = no.
So, you asked me to see my input. The first test I did was obviously
considering cut-offs, since I needed impose pbc = yes. These parameters are
the ones I sent you.
Of course plain cutoffs is not dealing well with the electrostatic part,
but in this case I was only doing just a quick test.
You said you have made calculations for a molecule of 50 atoms at a rate of
130ns/day on a single core. Did you used to that Gromacs 5? What are the
mdp options that you use in this case?
Eudes Eterno Fileti
Instituto de Ciência e Tecnologia da UNIFESP
Rua Talim, 330, São José dos Campos - SP
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