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?
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.
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
========================================
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--
========================================
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
========================================
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