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
--
========================================
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
