[gmx-users] nvt.gro

ram bio rmbio861 at gmail.com
Tue Sep 22 16:32:33 CEST 2009

Dear Gromacs Users,

I am following the justin tutorial on KALP-15 in lipid bilayer, I have a
query regarding the nvt.gro that is after the NVT equillibration phase. The
mdrun was proper without any warnings or errors, but when i visuallized the
nvt.gro in VMD, i found that the peptide is intact in between the bilayers,
but the the two layers got separated or else it is like the peptide bridging
the the two halves of the lipid bilayer with gap in between the layers and
also found few water molecules to the sides of the peptide or in the gap
mentioned betwwn the layers.

Please let me know is the simulation going on normally or there is an defect
or wrong going on, as the nvt equillibration was proper as i think i
continued for the next equillibration that is npt for 1ns.

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