Igor Marques
On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Igor Marques wrote: > > <snip> > > > 2. Can you post your .ndx file? >> for sn1 chain: >> >> Reading structure file >> Going to read 1 old index file(s) >> >> > Not exactly what I was going for (I wanted to see the contents of the .ndx > file), but... > > > 0 C12_&_r_1-72 : 72 atoms >> 1 C29_&_r_1-72 : 72 atoms >> 2 C30_&_r_1-72 : 72 atoms >> 3 C31_&_r_1-72 : 72 atoms >> 4 C32_&_r_1-72 : 72 atoms >> 5 C33_&_r_1-72 : 72 atoms >> 6 C34_&_r_1-72 : 72 atoms >> 7 C35_&_r_1-72 : 72 atoms >> 8 C36_&_r_1-72 : 72 atoms >> 9 C37_&_r_1-72 : 72 atoms >> 10 C38_&_r_1-72 : 72 atoms >> 11 C39_&_r_1-72 : 72 atoms >> 12 C40_&_r_1-72 : 72 atoms >> 13 C41_&_r_1-72 : 72 atoms >> 14 C42_&_r_1-72 : 72 atoms >> > > Here you only have 15 carbons. The sn-1 (palmitoyl) should be 16. > > > for sn2 chain: >> Reading structure file >> Going to read 1 old index file(s) >> >> 0 C9_&_r_1-72 : 72 atoms >> 1 C13_&_r_1-72 : 72 atoms >> 2 C14_&_r_1-72 : 72 atoms >> 3 C15_&_r_1-72 : 72 atoms >> 4 C16_&_r_1-72 : 72 atoms >> 5 C17_&_r_1-72 : 72 atoms >> 6 C18_&_r_1-72 : 72 atoms >> 7 C19_&_r_1-72 : 72 atoms >> 8 C20_&_r_1-72 : 72 atoms >> 9 C21_&_r_1-72 : 72 atoms >> 10 C22_&_r_1-72 : 72 atoms >> 11 C23_&_r_1-72 : 72 atoms >> 12 C24_&_r_1-72 : 72 atoms >> 13 C25_&_r_1-72 : 72 atoms >> 14 C26_&_r_1-72 : 72 atoms >> 15 C27_&_r_1-72 : 72 atoms >> 16 C28_&_r_1-72 : 72 atoms >> >> > And the same here - 17 groups instead of 18. I'm not familiar with the > numbering, but it seems odd to jump from, e.g., C9 to C13 - are you sure > your first carbon (C9) is not in the glycerol backbone rather than the > ester? > i'll also take a careful look into this! and the numbering is just like > this. don't ask! ;) > > 3. What is your command for the sn-2 chain? You cannot obtain >> unsaturated and saturated order parameters in the same command. You >> must do them separately, and the index groups are different. For >> instance, to get the order parameters around the unsaturation, your >> index file should contain only Cn-1, Cn, Cn+1, Cn+2, where Cn and >> Cn+1 are the C atoms joined by the double bond. Then run g_order >> with the -unsat option. These values can then replace the >> corresponding carbon positions in the g_order output of the whole >> sn-2 chain. If done improperly, you can get weird results. >> the command is actually the same with the apropriate index file... >> maybe this is the problem for POPC - i'll look at it carefully! >> >> > Then this is certainly a problem. > i'll look at it with my colleague. if our problem persists, we'll get back > in touch! > thanks again! ^^ > > >> 4. What are the simulation conditions? Are you trying to replicate >> the published work? Different simulations conditions will certainly >> impact the structural parameters, and insufficient sampling can give >> weird looking curves, as well. All it might mean is that your data >> are not yet well-converged. >> NPT, surface tension of 40 dyn/cm, t=310 K, GAFF force field. the >> plot represents the last 10 of 150 ns of production - however, it >> presents the same behavior in longer (200 ns) simulations! >> >> > I'd suspect the index file(s) and/or g_order commands rather than > convergence issues, in this case. > > -Justin > > >> thanks! >> >> -Justin >> >> >> best regards and thanks in advance! >> >> Igor Marques >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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 >
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