Teemu Murtola-3 wrote > Hi, > > On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko > <
> o.sushko@.ac > >wrote: > >> I'm want to analyse stratified layers of water around protein, >> so I provide next selection file to g_select: > > [clip] >> (shell2 is supposed to be a layer of whole water molecules from the layer >> 3 to 4 A) >> but it doesn't work correctly, moreover it even provides different >> results >> when just changing >> the order in 3rd line (shell2 = shell1 and shell), which shouldn't be the >> case. >> Interestingly, 1st and 2nd line separately works correctly. >> >> Even more interesting the next selection file works perfectly fine >> (regardless the order in 3rd line): >> [clip] >> > > Thanks for reporting this, this is clearly a bug. I have filed > http://redmine.gromacs.org/issues/1216 with some explanation of what > triggers the bug. > > (this also provides a layer between 3 and 4 A from protein, but some >> molecules are represented only by 1 or 2 atoms, which I want to avoid, >> that's why I'm using 'same residue as') >> > > There is probably no way to get exactly your condition before the bug is > fixed, but if you are OK with a slightly altered condition, you can do, > for > example, this (haven't tested, but should work): > > shell = group "SOL" and res_com within 0.4 of group "protein"; > shell1 = group "SOL" and not res_com within 0.3 of group "protein"; > shell2 = shell and shell1; > shell2; > > Best regards, > Teemu > -- > gmx-users mailing list > gmx-users@ > 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 > gmx-users-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists your suggestion with res_com works fine, although it results in less molecules for same shell compared to 'same residue as', but still keeps whole molecules in selection, which suits me. thanks a lot, Oleksandr -- View this message in context: http://gromacs.5086.n6.nabble.com/g-select-selection-file-problem-tp5006945p5006962.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
