[gmx-users] RE: Energy Minimization - not getting correct lipid area

[Justin A. Lemkul]

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

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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