Dear Amber users,
I am trying to perform a MD simulation of a membrane protein, for which the system includes lipids, H2O, and ions, generated by using Packmol-memgen found in the amber package. The energy of the total system seems to be strange, because the energy calculated by using Gromacs is very different from that of amber, for the latter of which is remarkably high in the bond, vdW, etc (gromacs is familiar for me).
Although I am a stranger of amber, I think that the pbc settings for lipids may be incorrect, bcause some atoms are slightly located in the outside from the periodical box. So, I want to ask you whether some (specific ?) settings for the pbs condition are required for pmemd.cuda in amber, or not. Thank you in adavance for your kind helps.
best regards,
Shin-ichi Kikuchi
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Received on Mon Jan 29 2024 - 01:00:02 PST
