[gmx-users] EM in kalp15_DPPC

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Aug 21 14:01:41 CEST 2012

 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?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, August 21, 2012 3:09 PM
Subject: Re: [gmx-users] EM in kalp15_DPPC

On 8/21/12 6:35 AM, Shima Arasteh wrote:
> Allright, I will check the configurations of out and inputs to find out the reason of warning.
> Please let me know something:
> Should I expect to see changes in area per lipids in each shrinking or it would happen after 25th repeat suddenly?

It will decrease steadily.  Make sure your loop is calling the correct coordinate file each time.  The energy-minimized output of the previous step is the input into the next iterations of shrinking, i.e.:

system_inflated.gro -> em_inflated.gro
em_inflated.gro -> system_shrink1.gro -> em_shrink1.gro
em_shrink1.gro -> system_shrink2.gro -> em_shrink2.gro


-- ========================================

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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