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.
-Justin
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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