[gmx-users] EM in kalp15_DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Aug 21 15:24:08 CEST 2012

 To remove the periodicity I ran the command trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact and chose "system" .
Is removing the periodicity something other than this? 
I don't have any idea to fix it here.:-(
It is just a way to repeat the tutorial from the begining!


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, August 21, 2012 5:00 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC

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

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