[gmx-users] RE: Energy Minimization - not getting correct lipid area
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 9 00:20:27 CEST 2012
On 6/8/12 6:18 PM, Erica Hicks wrote:
> Everything should be updated correctly. I added in the DPPC 128 underneath
> the protein in [molecules] but I still get the same results. What do you mean
> by " Further manual modifications are necessary based on how many lipids
> InflateGRO removes"? After I generated the new position restrain file, I
> updated the minim.mdp withe the correct info. I then scaled by a factor of 4,
> updated [molecules], ran energy minimization (mdrun -v -deffnm em), and
This is all my comment meant. If InflateGRO removes 4 lipids, then you have 124
left, which it sounds like you have accounted for.
> scaled by a factor 0.95. I have no idea what could possibly going wrong.
> Maybe something with the manipulation of InflateGRO????
Please provide the entire screen output of the first shrinking step that
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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