Dear Justin, I saw your tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html )
But my case is different. I can not even generate tpr file (trjconv as tutorial says) as it need box info Can you please suggest what can be the best possible way? If I just use system size dimension (X, Y Z) and do mimization it break my system in parts! How to choose optimum box vector in such case? regards, On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul <[email protected]> wrote: > > > On 6/14/13 7:37 PM, gromacs query wrote: > >> Dear Justin, >> >> Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I >> dont want to use as I think they are wrong). In my case if I have already >> water molecules in my system then if I use: >> >> editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic >> >> even now also I see pbc box (in vmd) its quite big than system as you can >> see from output >> >> system size : 10.707 11.077 7.493 (nm) >> diameter : 14.737 (nm) >> center : 6.928 6.932 6.936 (nm) >> box vectors : 0.000 0.000 0.000 (nm) >> box angles : 0.00 0.00 0.00 (degrees) >> box volume : 0.00 (nm^3) >> shift : 0.441 0.436 0.432 (nm) >> new center : 7.369 7.369 7.369 (nm) >> new box vectors : 14.737 14.737 14.737 (nm) >> new box angles : 90.00 90.00 90.00 (degrees) >> new box volume :3200.60 (nm^3) >> >> >> What should I do? >> >> > You're specifying a cubic box, but for most membrane systems, that's > probably wrong. What editconf is doing is determining what box vectors are > necessary, then since you're telling it to make the box cubic, it's forcing > all of the vectors to be the same. Apparently you have at least one > dimension that, in this case, is 14.737 nm in length, and then all other > vectors are then set to the same value. > > -Justin > > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
