[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:
> Hi,
> 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 
InflateGRO produces.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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