[gmx-users] nvt.gro

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 22 16:38:53 CEST 2009

ram bio wrote:
> 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.

You shouldn't continue blindly if you get weird results.  Please see the 
"Advanced Troubleshooting" page (part of the tutorial!), because I specifically 
address the issue of a bilayer separating:



> Ram
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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