[gmx-users] EM in kalp15_DPPC

[Shima Arasteh]

 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?



Sincerely,
Shima


----- 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>
Cc: 
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
etc.

-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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