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Order parameters calculation
- linxubo
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13 years 10 months ago #375
by linxubo
Order parameters calculation was created by linxubo
Hello!
Recently, I try to calculate order paramater for lipid(DPPC) tails. Although using proper index file, the output(sg-ang.xvg and sk-dist.xvg) of the tool g_order seems wrong. Noting that you analyse order parameters using other tools rather than g_order, I wonder whether your algorithm for calculating order parameters is the same as follows:
"Compute the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file has to contain a group with all equivalent atoms in all tails for each atom the order parameter has to be calculated for." (Here the atoms is similar to the CG beads)
and whether the tools you used can be free downloaded.
Thank you.
Recently, I try to calculate order paramater for lipid(DPPC) tails. Although using proper index file, the output(sg-ang.xvg and sk-dist.xvg) of the tool g_order seems wrong. Noting that you analyse order parameters using other tools rather than g_order, I wonder whether your algorithm for calculating order parameters is the same as follows:
"Compute the order parameter per atom for carbon tails. For atom i the vector i-1, i+1 is used together with an axis. The index file has to contain a group with all equivalent atoms in all tails for each atom the order parameter has to be calculated for." (Here the atoms is similar to the CG beads)
and whether the tools you used can be free downloaded.
Thank you.
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- djurre
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13 years 10 months ago #376
by djurre
Replied by djurre on topic Order parameters calculation
Hello linxubo,
As you mention g_order doesn't work with Martini, although I haven't figured out why.
The scripts do-order.sh and do-order-single.sh do work though. It is hardcoded to work with particular size lipids, as it will tell you if you run it without any arguments.
So, to answer your question: No it does not read an index file. It does calculate the P2 order parameter for every bond between beads.
As you mention g_order doesn't work with Martini, although I haven't figured out why.
The scripts do-order.sh and do-order-single.sh do work though. It is hardcoded to work with particular size lipids, as it will tell you if you run it without any arguments.
So, to answer your question: No it does not read an index file. It does calculate the P2 order parameter for every bond between beads.
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