Igor Marques
On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul <[email protected]> wrote: > > > Igor Marques wrote: > >> dear all, >> >> i've been trying to use g_order to analyse the disorder of the chains of >> POPC model membrane simulations, namely the SCD parameters. >> >> one example of "desired" output is this: >> 5IGl.png http://i.imm.io/5IGl.png - Performance of the general amber >> force field in modeling aqueous POPC membrane bilayers by Balázs Jójárt >> Tamás A. Martinek DOI: 10.1002/jcc.20748 >> >> >> however, my output, when plotted, presents a looks like mirrored: >> deuter.png >> http://i.imm.io/5IGK.png >> >> >> my input index files start with the first carbon after the c=o in each >> chain, as in the tutorial - >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html >> if started the other way around, the plot resembles published data... >> >> a colleague tried the same process with a DMPC membrane model and his >> plots are also mirrored. >> >> our command line: >> g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od >> OUTPUT_SCD.xvg >> >> what are we not doing/doing wrong? >> >> > A few questions: > > 1. What version of Gromacs is this? > version 4.5.3 > > 2. Can you post your .ndx file? > for sn1 chain: > Reading structure file Going to read 1 old index file(s) 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 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 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! > > 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! > 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 | (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/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 >
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