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
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Monday, 18 August 2014, 09:15PM +0430 from Justin Lemkul <[email protected]>:
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
[email protected] | (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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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