[gmx-users] g_order output is mirrored
Igor Marques
igor.dragon88 at gmail.com
Wed May 18 14:58:19 CEST 2011
dear all,
after justin contribution, the SN2 chain plot now looks a little different:
[image: sn2_new.png]
http://imm.io/5JAZ
the real matter of this e-mail, although i really appreciate the help justin
has provided regarding the proper use of this tool, is the fact that my plot
looks mirrored from the one i've previously referred, from Jojart and
Martinek --> http://i.imm.io/5IGl.png
forgetting, for now, the SN2 chain, harder to analyse, what i really found
weird is the fact that SN1 is mirroring the published results:
[image: sn1_new.png]
http://imm.io/5JCi
so, for segment 2, the first they analyze, in the filled triangle line the
value is around 0.35, while for the 14th segment the value is about 0.28. in
my case, the order is the other way around! my SN1 starts with a low value
that is increased through the chain! (0.24 --> 0.29).
should i change the order of the chain in the index files? although that
makes the plot resemble the ones already published, i don't think that is
the definitive solution to this problem!
(this applies also to the DMPC chains of my colleague)
best regards!
igor
Igor Marques
On Tue, May 17, 2011 at 9:47 PM, Igor Marques <igor.dragon88 at gmail.com>wrote:
>
> Igor Marques
>
>
> On Tue, May 17, 2011 at 9:42 PM, Justin A. Lemkul <jalemkul at 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
>>>
>>> ========================================
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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
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at 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
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>>
>
>
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