[gmx-users] problems in numbers of scale down by 0.95 in KALP in DPPC tutorial

[Justin Lemkul]

On 8/19/14, 8:39 AM, Mahboobe Sadr wrote:
>
> 00.  genrestr -f KALP_newbox_editconf.gro -o strong_posre.itp -fc 100000 100000
> 100000
>
> 01.  perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
>
> 02.  grompp -f minim.mdp -c system_inflated.gro -p topol.top -o confout.tpr
>
> 03.  mdrun -v -deffnm confout
>
> 04.  perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
> area_shrink1.dat
>
> 05.  grompp -f minim.mdp -c system_shrink1.gro  -p topol.top -o em_shrink1.tpr
>
> 06.  mdrun -v -deffnm em_shrink1
>
> 07.  perl inflategro.pl em_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5
> area_shrink2.dat
>
> 08.  grompp -f minim.mdp -c system_shrink2.gro -p topol.top -o em_shrink2.tpr
>
> 09.  mdrun -v -deffnm em_shrink2
>
> 10.  perl inflategro.pl em_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5
> area_shrink3.dat
>
> 11.  grompp -f minim.mdp -c system_shrink3.gro -p topol.top -o em_shrink3.tpr
>
> 12.  mdrun -v -deffnm em_shrink3
>
> 13.  perl inflategro.pl em_shrink3.gro 0.95 DPPC 0 system_shrink4.gro 5
> area_shrink4.dat
>
>            part of result :
>
>            Area per protein: 2 nm^2
>            Area per lipid: 6.93639237588421 nm^2
>
>            Area per protein, upper half: 1.75 nm^2
>            Area per lipid, upper leaflet :      6.94036062985246 nm^2
>
>            Area per protein, lower half: 2 nm^2
>            Area per lipid, lower leaflet : 6.93639237588421 nm^2
>

6.9 nm^2 is not equal to 69 A^2.  It is 690 A^2.

-Justin

> 14.  grompp -f minim.mdp -c system_shrink4.gro -p topol.top -o em_shrink4.tpr
>
> 15.  mdrun -v -deffnm em_shrink4
>
> --
> Sent from myMail app for Android
>
> Monday, 18 August 2014, 09:15PM +0430 from Justin Lemkul <jalemkul at vt.edu>:
>
> On 8/18/14, 10:06 AM, Mahboobe Sadr wrote:
>  >
>  > Dear all,
>  > I am new in gromacs and specially in MD simulation of membrane protein,
> in   part "define box and solvent" of justin's tutorial , in scaling down the
> lipids,  I reached an area per lipid of ~69 A^2, after 4 times instead of 26
> times....
>  > I don't know ,where I made a mistake?
>
> Without seeing your exact commands and the corresponding output, there's nothing
> to say.  If you scale each time by 0.95, it is mathematically impossible to
> arrive at a proper APL in this system with only 4 iterations.  At least one of
> your commands or preparation steps was wrong; the outcome is extremely reproducible.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================