Hi Justin, Thanks for comments, On Thu, Aug 13, 2009 at 8:21 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Jamie Seyed wrote: > >> Hi all, >> Thanks for your comments. Actually as Vitaly mentioned I am still try to >> visualize the gro-file made by genbox. I found out for any number that I use >> for "-nmol ? -ci insert.gro" after some iterations and upto these values: >> Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 >> System total charge: 0.000 >> I get segmentation fault. In fact cut-off values from 0.1 in the case of >> -nmol 0, jumps to 0.45 in the case of -nmol 1 and then it gives me >> segmentation fault. The only way to get rid of it is put -nmol 0! >> Now my questions are: >> (1) What can be wrong in my insert.gro file. Does it matter the >> coordinates of 1 molecule that I obtained from spc216.gro file?? The format >> is the same. >> > > Can you post your exact command line? my command is: genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro I also tried genbox -cp f.gro -cs spc216.gro -o f_b4em.pdb -p topol.top -shell 0.5 -nmol 1 -ci insert.gro -try 100 by using 20,30,40...,100 but each time was the same. (I also did it without shell command but no success) > > (2) This command will try to add water where? In the same coordinates as >> insert.gro?? >> > > From genbox -h: > > "3) Insert a number (-nmol) of extra molecules (-ci) at random positions. > The > program iterates until nmol molecules have been inserted in the box. To > test > whether an insertion is successful the same VanderWaals criterium is used > as > for removal of solvent molecules. When no appropriately sized holes (holes > that can hold an extra molecule) are available the program tries for -nmol > * > -try times before giving up. Increase -try if you have several small holes > to > fill." > -Justin > > What is your suggestions?? Many Thanks in Advance/Jamie >> >> On Thu, Aug 13, 2009 at 5:25 PM, Vitaly V. Chaban <[email protected]<mailto: >> [email protected]>> wrote: >> >> Tsjerk, >> >> I understood the situation in such a way that MD was not run at all, >> so Jamie visualizes *gro* file obtained with *genbox*... >> >> Jamie, >> didn't you look at this: http://www.ime.unicamp.br/~martinez/packmol/ >> to prepare your system? >> >> >> Vitaly >> >> >> > >> >> Thanks for the answer. When I said far away means my pore was in >> one corner >> >> of vmd window and the water molecules in opposite corner (almost). >> > >> > Did I miss something or did neither Vitaly nor Justin reply "Are you >> > perhaps seeing the effect of periodic boundary conditions?". >> > >> > Tsjerk >> > >> > -- >> > Tsjerk A. Wassenaar, Ph.D. >> > Junior UD (post-doc) >> > Biomolecular NMR, Bijvoet Center >> > Utrecht University >> > Padualaan 8 >> > 3584 CH Utrecht >> > The Netherlands >> > P: +31-30-2539931 >> > F: +31-30-2537623 >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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