On 8/21/12 8:01 AM, Shima Arasteh wrote:
Thanks for your reply.
In order to check the warning of grompp after scaling up I ran grompp again
without -maxwarn:
grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr
WARNING 1 [file minim.mdp]:
The sum of the two largest charge group radii (3.840099) is larger than
rlist (1.200000).
Do I need to change the minim.mdp settings? Visualizing the system doesn't show
any odd result!
Would you mind helping me?
Likely you did not correctly remove the periodicity of the DPPC membrane before
inflating so you have fragmented molecules somewhere. Go back and fix it
according to the instructions provided in the tutorial.
-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
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