<br clear="all"> Igor Marques<br>
<br><br><div class="gmail_quote">On Tue, May 17, 2011 at 8:04 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Igor Marques wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
dear all,<br>
<br>
i've been trying to use g_order to analyse the disorder of the chains of POPC model membrane simulations, namely the SCD parameters.<br>
<br>
one example of "desired" output is this:<br></div><div class="im">
5IGl.png <a href="http://i.imm.io/5IGl.png" target="_blank">http://i.imm.io/5IGl.png</a> - Performance of the general amber force field in modeling aqueous POPC membrane bilayers by Balázs Jójárt Tamás A. Martinek DOI: 10.1002/jcc.20748<br>
<br>
<br>
however, my output, when plotted, presents a looks like mirrored:<br></div><div class="im">
deuter.png<br>
<a href="http://i.imm.io/5IGK.png" target="_blank">http://i.imm.io/5IGK.png</a><br>
<br>
<br>
my input index files start with the first carbon after the c=o in each chain, as in the tutorial - <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/tutorial.html</a><br>
if started the other way around, the plot resembles published data...<br>
<br>
a colleague tried the same process with a DMPC membrane model and his plots are also mirrored.<br>
<br>
our command line:<br>
g_order -f ../TRAJECTORY.xtc -s ../TOPOLOGY.tpr -n INDEX_CHAIN_sn1.ndx -od OUTPUT_SCD.xvg<br>
<br>
what are we not doing/doing wrong?<br>
<br>
</div></blockquote>
<br>
A few questions:<br>
<br>
1. What version of Gromacs is this?<br>
version 4.5.3<br></blockquote><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
2. Can you post your .ndx file?<br>
for sn1 chain:<br></blockquote><div>Reading structure file</div><div>Going to read 1 old index file(s)</div><div><br></div><div> 0 C12_&_r_1-72 : 72 atoms</div><div> 1 C29_&_r_1-72 : 72 atoms</div>
<div> 2 C30_&_r_1-72 : 72 atoms</div><div> 3 C31_&_r_1-72 : 72 atoms</div><div> 4 C32_&_r_1-72 : 72 atoms</div><div> 5 C33_&_r_1-72 : 72 atoms</div><div> 6 C34_&_r_1-72 : 72 atoms</div>
<div> 7 C35_&_r_1-72 : 72 atoms</div><div> 8 C36_&_r_1-72 : 72 atoms</div><div> 9 C37_&_r_1-72 : 72 atoms</div><div> 10 C38_&_r_1-72 : 72 atoms</div><div> 11 C39_&_r_1-72 : 72 atoms</div>
<div> 12 C40_&_r_1-72 : 72 atoms</div><div> 13 C41_&_r_1-72 : 72 atoms</div><div> 14 C42_&_r_1-72 : 72 atoms </div><div><br></div><div>for sn2 chain:</div><div><div>Reading structure file</div>
<div>Going to read 1 old index file(s)</div><div><br></div><div> 0 C9_&_r_1-72 : 72 atoms</div><div> 1 C13_&_r_1-72 : 72 atoms</div><div> 2 C14_&_r_1-72 : 72 atoms</div><div>
3 C15_&_r_1-72 : 72 atoms</div>
<div> 4 C16_&_r_1-72 : 72 atoms</div><div> 5 C17_&_r_1-72 : 72 atoms</div><div> 6 C18_&_r_1-72 : 72 atoms</div><div> 7 C19_&_r_1-72 : 72 atoms</div><div> 8 C20_&_r_1-72 : 72 atoms</div>
<div> 9 C21_&_r_1-72 : 72 atoms</div><div> 10 C22_&_r_1-72 : 72 atoms</div><div> 11 C23_&_r_1-72 : 72 atoms</div><div> 12 C24_&_r_1-72 : 72 atoms</div><div> 13 C25_&_r_1-72 : 72 atoms</div>
<div> 14 C26_&_r_1-72 : 72 atoms</div><div> 15 C27_&_r_1-72 : 72 atoms</div><div> 16 C28_&_r_1-72 : 72 atoms</div></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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.<br>
the command is actually the same with the apropriate index file... maybe this is the problem for POPC - i'll look at it carefully!<br></blockquote><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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.<br>
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!<br></blockquote><div><br></div>
<div>thanks!</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
best regards and thanks in advance!<br>
<br>
Igor Marques<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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