[gmx-users] EM in kalp15_DPPC

[Justin Lemkul]

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

-- 
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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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