Dear Justin, After 20 iterations I've obtained structure like this http://www.sendspace.com/file/gyyj38
I suppose that this variat is more closely to correct form :) But during solvation via GenBox I've obtained that error One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. Where I can change that cut-off distance? James 2011/10/17 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Ok, James thank you >> >> It seems that I should to wite some script for too many iterations e.g >> >> perl inflategro.pl <http://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 <http://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 <http://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 >> >> > All of which can be done in a for-loop instead of typing it out manually. > > > 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 >> >> > Yes. You can read that value from the screen or from the area.dat file > that inflategro.pl prints. > > > -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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