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Analysis for the trajectory
#28150 08/16/11 11:15 AM
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Ramya Offline OP
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Is there any other analysis that can be performed for the MC simulation trajectory apart from structural motif and energy surface calculation?


Ramya.L.
Re: Analysis for the trajectory
Ramya #28151 08/16/11 11:25 AM
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Well, yes, but what is it that you want to know? Usually one has a question or an hypotehsis that one wants to resolve or test using a simulation.


Lennart Nilsson
Karolinska Institutet
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Re: Analysis for the trajectory
lennart #28152 08/16/11 11:32 AM
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Ramya Offline OP
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I tried to find the conformation of the peptide whether it forms secondary structures or not using usual phi-psi plot, motif analysis and by drawing energy landscape (using Pcoor). I want to further emphasize the results obtained from these analysis by other permissible method.

Thanks in advance for any suggestions/comments.


Ramya.L.
Re: Analysis for the trajectory
Ramya #28153 08/16/11 11:37 AM
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The CHARMM command
COOR SECStructure (corman.doc)
in a CHARMM loop can be used to find the fraction of residues that are in an alpha-helical or beta-strand conformation during your simulation.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Analysis for the trajectory
lennart #28154 08/16/11 11:38 AM
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Ramya Offline OP
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Thanks. But the simulation is completed, can I try it for the trajectory separately? Is it possible? (because the flag is like during the dynamics)

Last edited by Ramya; 08/16/11 11:42 AM.

Ramya.L.
Re: Analysis for the trajectory
Ramya #28155 08/16/11 11:48 AM
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???
All trajectory analysis in CHARMM is performed on the trajectory stored on disk. This is no exception.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Analysis for the trajectory
lennart #28156 08/16/11 11:59 AM
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Ramya Offline OP
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Ok. Thanks. I will try it.


Ramya.L.

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