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 -- Sent from myMail app for Android 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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
