Ok, James thank you It seems that I should to wite some script for too many iterations e.g
perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr mdrun -v -deffnm minimized2 perl inflategro.pl minimized2.gro 0.95 DPPC 0 shrinked2.gro 5 area_shrink1.dat grompp -f minim.mdp -c shrinked2.gro -p topol.top -o minimized3.tpr mdrun -v -deffnm minimized2 ...... perl inflategro.pl minimized20.gro 0.95 DPPC 0 shrinked20.gro 5 area_shrink1.dat grompp -f minim.mdp -c shrinked20.gro -p topol.top -o minimized21.tpr mdrun -v -deffnm minimized21 Does this action sequence correct? So as the consequence I need to find operator wich stop the script untill defined value of S per lipid will be reached Thanks again James 2011/10/17 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> >> James, >> >> As the consequence the correct orientation of the peptide in the membrane >> as well as futher solvation are caused many questions :) >> >> >> Firsly, following by tutorial guide I've done orientation of KALP peptide >> in the membrane by >> >> 1- perl inflategro.pl <http://inflategro.pl/> confout.gro 0.95 DPPC 0 >> system_shrink1.gro 5 area_shrink1.dat >> 2- minimization >> 3- perl inflategro.pl <http://inflategro.pl/> system.gro 4 DPPC 14 >> system_inflated.gro 5 area.dat >> >> >> >> >> 4- minimization >> >> after six iterations of the 3rd and 4th steps I've obtained 6,5 nm^2 >> value for the area per lipid >> >> > The tutorial suggests at least 26 or so iterations. Your APL value is 100 > times larger than it should be. > > > Next I've done solvation of my protein ( including big vdv radii for >> carbons ) >> >> >> >> Finally my sytem is consisted of 70000 atoms. I think that it's too big >> ammount of water molecules for such small protein like KALP >> >> > Yes, because your membrane is not correctly packed. > > > so its seems that i've done some mistakes- >> 1- During shrinking of my peptide- I think that obtained structure ( >> http://www.sendspace.com/**file/wenkf4<http://www.sendspace.com/file/wenkf4>) >> consist of too big distances beetween peptides so it should be futher >> shrinked. >> >> > Correct. > > > >> >> But how many iterations must be? I've found in the tutorial that 65 A^2 is >> good value for that system. But maybe I've used wrong parametries in the pl >> program? >> >> > No, you just haven't done enough iterations. See above. Your value is 6.5 > nm^2 , which is 6500 A^2. > > > 2- Or maybe too many waters are moved within the membrane in spite of >> increased VDV radius for carbon atoms. So what I should do for the excluding >> all unnecessary water from my structure? >> >> >> > Ignore this for now. Your system simply isn't built correctly. > > > >> E.g I want to simulate hydrophobic effect. What length of that simulation >> must be ? >> > > Perhaps tens of ns. > > > How I can evaluate the ammount of water before and after simulations? >> > > Visualization. > > > Finally, What other options of Genbox could I use for preventing insertion >> of water into my membrane ? >> >> >> > None. A better starting model is required. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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