Re: SV: SV: SV: [gmx-users] g_saltbr

> report or are you doing it since you understand the code? > > Thank you all! > Sarah > > > > Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar > Sendt: on 02-12-2009 19:29 > Til: jalem...@vt.edu; Discussion list for GRO

SV: SV: SV: SV: [gmx-users] g_saltbr

-2009 19:29 Til: jalem...@vt.edu; Discussion list for GROMACS users Emne: Re: SV: SV: SV: [gmx-users] g_saltbr Hi, Of course the real answer is in the code... if (bSep) { snew(buf,256); for(i=0; (iresname[resnr]),resnr+1); cg[ncg].label=strdup(buf); Althogether, this just means

SV: SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: > In each of the files are a set of distances as a function of time - it does > not seem that strange, that the size is equal then. > > When I plot for instance the four .xvg files mentioned above I get four > different curves. Also "diff" lists that every line is differe

Re: SV: SV: SV: [gmx-users] g_saltbr

Hi, Of course the real answer is in the code... if (bSep) { snew(buf,256); for(i=0; (iresname[resnr]),resnr+1); cg[ncg].label=strdup(buf); Althogether, this just means that you have multiple charge(d) groups per residue, which are assigned the same label. Let's see, a phosphate a

Re: SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: In each of the files are a set of distances as a function of time - it does not seem that strange, that the size is equal then. When I plot for instance the four .xvg files mentioned above I get four different curves. Also "diff" lists that every line is different. I

SV: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: >Per the documentation, the only options that can be passed to g_saltbr are > -s >and -f, so no, you cannot use any index groups. > > I thought so :-( > Indeed, Mark's clever suggestion may be useful here. Yes, definitely. > There are no old xvg files in t

Re: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: Per the documentation, the only options that can be passed to g_saltbr are -s and -f, so no, you cannot use any index groups. I thought so :-( Indeed, Mark's clever suggestion may be useful here. There are no old xvg files in the directory. I have used "rm -r

Re: SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: Then I run the command again with -sep to get the individual graphs of each interaction. This is unfortunately a rather tedious exercise since very many files are generated for all sort of charged interactions (DMPC-DMPC, smallmolecule-smallmolecule, counterion-counterion, an

SV: SV: [gmx-users] g_saltbr

Sarah Witzke wrote: > Dear gmx users, > > > > I'm sorry to continue an old thread - here's a summary: > > I have a DMPC bilayer surrounded by water and a small organic molecule with a > deprotonated carboxylic acid. The small molecule diffuses near the membrane > interface/into the membrane. I woul