[gmx-users] EM in kalp15_DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Aug 21 19:12:09 CEST 2012

I visualized the dppc128.gro and dppc128_whole.gro. The dppc seems to get smaller and more compact in dppc128_whole.gro than the dppc128.gro. 
I think it's normal!


From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org 
Sent: Tuesday, August 21, 2012 6:00 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC

On 8/21/12 9:24 AM, Shima Arasteh wrote:
>   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?

That's the correct command.  The differences between dppc128.gro and 
dppc128_whole.gro should be fairly apparent when visualized.

> I don't have any idea to fix it here.:-(
> It is just a way to repeat the tutorial from the begining!

I doubt you have to start completely over, but I know the protocol works as 
advertised.  If molecules are still split (which is likely the case, given the 
error below), spotting them in the inflated system should be fairly easy with 
visualization.  That should help you track down what's gone wrong.


> Sincerely,
> Shima
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> 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


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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