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

Mahboobe Sadr sadr.mahboobe1989 at gmail.com
Tue Aug 19 14:39:21 CEST 2014

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
14.  grompp -f minim.mdp -c system_shrink4.gro -p topol.top -o em_shrink4.tpr
15.  mdrun -v -deffnm em_shrink4

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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 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

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