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script for order parameter doesn't work
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10 years 3 months ago #3451
by Ganjali
script for order parameter doesn't work was created by Ganjali
Hi,
Dear Siewert, I have a problem with order parameter script, i downloaded and placed it on my directory and used this command (./do-order.py 0 10000 20 0 0 1 64 DSPC) but i have obtained this result (./do-order.py: /user/bin/python^M: bad interpreter: No such file or directory), what is the problem? what must i do?
Many thanks,
Mokhtar
Dear Siewert, I have a problem with order parameter script, i downloaded and placed it on my directory and used this command (./do-order.py 0 10000 20 0 0 1 64 DSPC) but i have obtained this result (./do-order.py: /user/bin/python^M: bad interpreter: No such file or directory), what is the problem? what must i do?
Many thanks,
Mokhtar
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10 years 3 months ago #3453
by Clement
Replied by Clement on topic script for order parameter doesn't work
You do not have python installed... Install one python interpreter from the versions 2.x (not 3.x).
(P.S.: no need to post your question many times... We have a strict moderation policy on the Forum because of a lot of annoying SPAM recently; sorry for the delay...)
(P.S.: no need to post your question many times... We have a strict moderation policy on the Forum because of a lot of annoying SPAM recently; sorry for the delay...)
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10 years 3 months ago #3461
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Hi,
Dear Siewert, i installed python-2.5.6 and this program is in bin, i am in the same directory that all files is therein, and i used again this command (./do-order.py 0 10000 20 0 0 1 64 DSPC) but it doesn't work and i obtained the same results.I tested python-2.5.6 with this command (python -h ), this program have been installed. what is the problem? what must i do?
Regards,
Ganjali
Dear Siewert, i installed python-2.5.6 and this program is in bin, i am in the same directory that all files is therein, and i used again this command (./do-order.py 0 10000 20 0 0 1 64 DSPC) but it doesn't work and i obtained the same results.I tested python-2.5.6 with this command (python -h ), this program have been installed. what is the problem? what must i do?
Regards,
Ganjali
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10 years 3 months ago #3462
by Clement
Replied by Clement on topic script for order parameter doesn't work
Try to type: python do-order.py 0 10000 20 0 0 1 64 DSPC
It's probably coming from the "#!/user/bin/python" in the headers, which doesn't make any sense.
It's probably coming from the "#!/user/bin/python" in the headers, which doesn't make any sense.
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10 years 3 months ago - 10 years 3 months ago #3464
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Hi,
Dear Siewert, I performed this command that you mentioned (python do-order.py 0 10000 20 0 0 1 64 DSPC ),I was obtained this result ( Compute (second rank) order parameter, defined as:
P2 = 0.5*(3*<cosآ²(theta)> - 1)
where "theta" is the angle between the bond and the bilayer normal.
P2 = 1 perfect alignement with the bilayer normal
P2 = -0.5 anti-alignement
P2 = 0 random orientation
All lipids defined in the "martini_v2.0_lipids.itp" file can be analyzed
with this script.
Usage: do-order.py <traj file> <initial time> <final time> <skip frames> <bilayer normal - xyz> <#lipids> <lipid type>
> do-order.py traj.xtc 0 10000 5 0 1 0 64 DSPC
will for example read a 10ns trajectory of 64 DSPC lipids, calculating the order parameter for
every 5th frame and averaging the results. P2 will be calculated relative to the y-axis.
WARNING script will output all frames in one go, into files called frame_dump_XXX.gro and
then remove them so don't have any other files with this name in the current directory.), and didn't produce any new file. what must i do?
Many thanks,
Mokhtar
Dear Siewert, I performed this command that you mentioned (python do-order.py 0 10000 20 0 0 1 64 DSPC ),I was obtained this result ( Compute (second rank) order parameter, defined as:
P2 = 0.5*(3*<cosآ²(theta)> - 1)
where "theta" is the angle between the bond and the bilayer normal.
P2 = 1 perfect alignement with the bilayer normal
P2 = -0.5 anti-alignement
P2 = 0 random orientation
All lipids defined in the "martini_v2.0_lipids.itp" file can be analyzed
with this script.
Usage: do-order.py <traj file> <initial time> <final time> <skip frames> <bilayer normal - xyz> <#lipids> <lipid type>
> do-order.py traj.xtc 0 10000 5 0 1 0 64 DSPC
will for example read a 10ns trajectory of 64 DSPC lipids, calculating the order parameter for
every 5th frame and averaging the results. P2 will be calculated relative to the y-axis.
WARNING script will output all frames in one go, into files called frame_dump_XXX.gro and
then remove them so don't have any other files with this name in the current directory.), and didn't produce any new file. what must i do?
Many thanks,
Mokhtar
Last edit: 10 years 3 months ago by Ganjali.
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10 years 3 months ago - 10 years 3 months ago #3465
by Clement
Replied by Clement on topic script for order parameter doesn't work
What are you trying to analyze? What files are present in the current directory?
Last edit: 10 years 3 months ago by Clement.
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10 years 3 months ago #3466
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Hi,
I'm trying to Deuterium order parameter, and i'm in the same directory that every files is therein from the beginning (.xtc, .tpr, .gro ,...... ).
Thanks,
Mokhtar
I'm trying to Deuterium order parameter, and i'm in the same directory that every files is therein from the beginning (.xtc, .tpr, .gro ,...... ).
Thanks,
Mokhtar
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10 years 3 months ago #3467
by Clement
Replied by Clement on topic script for order parameter doesn't work
I honestly have no clue. I lack a lot of information here... I assume you're following the Martini tutorial, right? Did you check your trajectory wasn't empty? Your command line seems to include what's expected, in the right order. Did you really simulate DSPC? I need more steps than what you give me; can't guess what's wrong with just what you said so far.
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10 years 3 months ago - 10 years 3 months ago #3468
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Dear Siewert, I'm simulating DSPC according to your tutorial and command, I'm sure. I tried again with this command (python do-order.py traj.xtc 0 10000 20 0 0 1 64 DSPC) and i obtained a order.dat file with these characteristics:
Frame NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1A GL2-C1B C1A-C2A C2A-C3A C3A-C4A C4A-C5A C1B-C2B C2B-C3B C3B-C4B C4B-C5B
0 -0.173 0.609 -0.148 0.526 0.434 0.441 0.425 0.262 0.100 0.436 0.399 0.322 0.185
1 -0.077 0.639 -0.189 0.475 0.400 0.353 0.324 0.136 0.151 0.290 0.274 0.284 0.260
2 -0.182 0.593 -0.228 0.552 0.451 0.476 0.383 0.267 0.067 0.519 0.416 0.277 0.113
3 -0.051 0.527 -0.172 0.446 0.433 0.495 0.452 0.337 0.102 0.451 0.403 0.220 0.146
4 -0.180 0.638 -0.168 0.493 0.451 0.411 0.474 0.335 0.226 0.462 0.267 0.213 0.129
5 -0.078 0.579 -0.285 0.494 0.430 0.468 0.440 0.347 0.211 0.381 0.383 0.278 0.157
6 -0.103 0.634 -0.290 0.492 0.477 0.405 0.399 0.199 0.253 0.357 0.360 0.210 0.132
7 -0.057 0.562 -0.196 0.533 0.543 0.505 0.469 0.291 0.072 0.508 0.455 0.314 0.190
8 -0.106 0.606 -0.156 0.449 0.468 0.472 0.426 0.258 0.131 0.423 0.351 0.275 0.240
9 -0.139 0.591 -0.227 0.479 0.503 0.432 0.326 0.253 0.208 0.385 0.297 0.249 0.128
10 -0.146 0.627 -0.194 0.536 0.399 0.463 0.336 0.238 0.189 0.435 0.346 0.252 0.163
11 -0.183 0.626 -0.247 0.430 0.349 0.444 0.370 0.312 0.206 0.358 0.377 0.181 0.164
12 -0.095 0.616 -0.228 0.516 0.355 0.412 0.427 0.233 0.096 0.346 0.356 0.276 0.229
13 -0.113 0.653 -0.181 0.462 0.386 0.488 0.409 0.318 0.158 0.464 0.333 0.216 0.161
14 -0.147 0.554 -0.200 0.501 0.303 0.519 0.448 0.315 0.171 0.356 0.380 0.305 0.123
15 -0.102 0.619 -0.199 0.500 0.395 0.452 0.420 0.329 0.204 0.347 0.344 0.229 0.086
16 -0.023 0.635 -0.211 0.503 0.447 0.444 0.435 0.245 0.121 0.490 0.360 0.156 0.107
average -0.115 0.606 -0.207 0.493 0.425 0.452 0.410 0.275 0.157 0.412 0.359 0.251 0.160
Abs average order parameters for carbon chains <Sn> = 0.339
what do you think about this command? is it true? are the results the same with your results?
Kind regards,
Mokhtar
Frame NC3-PO4 PO4-GL1 GL1-GL2 GL1-C1A GL2-C1B C1A-C2A C2A-C3A C3A-C4A C4A-C5A C1B-C2B C2B-C3B C3B-C4B C4B-C5B
0 -0.173 0.609 -0.148 0.526 0.434 0.441 0.425 0.262 0.100 0.436 0.399 0.322 0.185
1 -0.077 0.639 -0.189 0.475 0.400 0.353 0.324 0.136 0.151 0.290 0.274 0.284 0.260
2 -0.182 0.593 -0.228 0.552 0.451 0.476 0.383 0.267 0.067 0.519 0.416 0.277 0.113
3 -0.051 0.527 -0.172 0.446 0.433 0.495 0.452 0.337 0.102 0.451 0.403 0.220 0.146
4 -0.180 0.638 -0.168 0.493 0.451 0.411 0.474 0.335 0.226 0.462 0.267 0.213 0.129
5 -0.078 0.579 -0.285 0.494 0.430 0.468 0.440 0.347 0.211 0.381 0.383 0.278 0.157
6 -0.103 0.634 -0.290 0.492 0.477 0.405 0.399 0.199 0.253 0.357 0.360 0.210 0.132
7 -0.057 0.562 -0.196 0.533 0.543 0.505 0.469 0.291 0.072 0.508 0.455 0.314 0.190
8 -0.106 0.606 -0.156 0.449 0.468 0.472 0.426 0.258 0.131 0.423 0.351 0.275 0.240
9 -0.139 0.591 -0.227 0.479 0.503 0.432 0.326 0.253 0.208 0.385 0.297 0.249 0.128
10 -0.146 0.627 -0.194 0.536 0.399 0.463 0.336 0.238 0.189 0.435 0.346 0.252 0.163
11 -0.183 0.626 -0.247 0.430 0.349 0.444 0.370 0.312 0.206 0.358 0.377 0.181 0.164
12 -0.095 0.616 -0.228 0.516 0.355 0.412 0.427 0.233 0.096 0.346 0.356 0.276 0.229
13 -0.113 0.653 -0.181 0.462 0.386 0.488 0.409 0.318 0.158 0.464 0.333 0.216 0.161
14 -0.147 0.554 -0.200 0.501 0.303 0.519 0.448 0.315 0.171 0.356 0.380 0.305 0.123
15 -0.102 0.619 -0.199 0.500 0.395 0.452 0.420 0.329 0.204 0.347 0.344 0.229 0.086
16 -0.023 0.635 -0.211 0.503 0.447 0.444 0.435 0.245 0.121 0.490 0.360 0.156 0.107
average -0.115 0.606 -0.207 0.493 0.425 0.452 0.410 0.275 0.157 0.412 0.359 0.251 0.160
Abs average order parameters for carbon chains <Sn> = 0.339
what do you think about this command? is it true? are the results the same with your results?
Kind regards,
Mokhtar
Last edit: 10 years 3 months ago by Ganjali.
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10 years 3 months ago #3471
by Clement
Replied by Clement on topic script for order parameter doesn't work
The results depends on your simulation... Seems fine to me. Are you sure the bilayer normal is along the z axis?
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10 years 3 months ago #3473
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Dear Siewert, Thank you for your attention, I'm not sure that bilayer normal is along the Z axis, how can i know about this? can you give me it's command? I want to know about it.
sincerely,
Mokhtar
sincerely,
Mokhtar
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10 years 2 months ago #3477
by Clement
Replied by Clement on topic script for order parameter doesn't work
If you check your final conformation, which axis amongst {x,y,z} is perpendicular of the plane of the membrane? No command line, just visualization.
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10 years 2 months ago #3478
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Hi,
I saw final conformation, bilayer normal is along Z axis, many thanks.
I have a question about MSD,I used this command for it (g_msd -f traj.xtc -s topol.tpr -n index.ndx -rmcomm -beginfit -1 -endfit -1 -lateral Z), after this command i selected DSPC group for calculating the it's MSD and i don't know which group must i select for center of mass removal.
Regards,
Mokhtar
I saw final conformation, bilayer normal is along Z axis, many thanks.
I have a question about MSD,I used this command for it (g_msd -f traj.xtc -s topol.tpr -n index.ndx -rmcomm -beginfit -1 -endfit -1 -lateral Z), after this command i selected DSPC group for calculating the it's MSD and i don't know which group must i select for center of mass removal.
Regards,
Mokhtar
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10 years 2 months ago #3479
by Clement
Replied by Clement on topic script for order parameter doesn't work
Same group.
You need to tune your use of -beginfit -endfit though... They must correspond to the linear part of your MSD curve, or the results you'll obtain won't make any sense. Plot it once like that, you'll see what I mean. Then you can define a bit more finely the boundaries you need to use.
You need to tune your use of -beginfit -endfit though... They must correspond to the linear part of your MSD curve, or the results you'll obtain won't make any sense. Plot it once like that, you'll see what I mean. Then you can define a bit more finely the boundaries you need to use.
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10 years 2 months ago #3481
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Dear Siewert, I gave D[ DSPC]= 6.30 *10^-7 (cm^2/s), Is it the same your result?
Thanks,
Mokhtar
Thanks,
Mokhtar
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10 years 2 months ago #3483
by Clement
Replied by Clement on topic script for order parameter doesn't work
No idea, don't have simulations to quickly check that. But it looks like a value one could obtain for Martini lipid... Did you make sure to fit only the linear part of the MSD plot?
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10 years 2 months ago #3484
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
I used this command (g_msd -f traj.xtc -s topol.tpr -n index.ndx -rmcomm -beginfit -1 -endfit -1 -lateral Z) and i selected the same group, how can i fit just linear part of MSD? I saw output file and i understood which part of MSD curve is linear, but i don't know how to fit this part of MSD curve.
Thanks,
Mokhtar
Thanks,
Mokhtar
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10 years 2 months ago - 10 years 2 months ago #3485
by Clement
Replied by Clement on topic script for order parameter doesn't work
Dear Mokhtar,
I assume you're following the Martini tutorials presented on this site. All the necessary commands are listed there. But the help of any GROMACS command can be invoked with the "-f " flag, and I think your questions are a bit beyond the goal of this Forum, and more fit for the GROMACS' FAQ. Read the manuals of the commands you use, everything will be more clear.
The help of g_msd (g_msd -h) returns:
Thanks,
Clément
I assume you're following the Martini tutorials presented on this site. All the necessary commands are listed there. But the help of any GROMACS command can be invoked with the "-f " flag, and I think your questions are a bit beyond the goal of this Forum, and more fit for the GROMACS' FAQ. Read the manuals of the commands you use, everything will be more clear.
The help of g_msd (g_msd -h) returns:
You need to tune the values you pass to the -beginfit and -endfit flags, limiting your fit to the linear regime of the MSD plot you obtain.The diffusion coefficient is determined by linear regression of the MSD, where, unlike for the normal output of D, the times are weighted according to the number of reference points, i.e. short times have a higher weight. Also when -beginfit=-1, fitting starts at 10% and when -endfit=-1, fitting goes to 90%. Using this option one also gets an accurate error estimate based on the statistics between individual molecules. Note that this diffusion coefficient and error estimate are only accurate when the MSD is completely linear between -beginfit and -endfit.
Thanks,
Clément
Last edit: 10 years 2 months ago by Clement.
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10 years 2 months ago - 10 years 2 months ago #3486
by Ganjali
Replied by Ganjali on topic script for order parameter doesn't work
Dear Clement, Many thanks for your attention.
Regards,
Mokhtar
Regards,
Mokhtar
Last edit: 10 years 2 months ago by Ganjali.
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