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Water Molecule occupancy at a position?
#13454 02/14/07 09:21 PM
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Hi,

Would you like to suggest how to analysis the water molecule's occpuancy
at a speical position during the MD simulations?

Thanks.

Re: Water Molecule Occpuancy at a position?
zhangxd68 #13455 02/14/07 09:28 PM
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The CORRel module (correl.doc) can be used for an individual water molecule - eg to get its position or distance from a point vs time. To obtain a density map you can use COOR ANALysis (corman.doc).


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Water Molecule Occpuancy at a position? *DELETED*
lennart #13456 02/14/07 09:47 PM
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Thanks.

Last edited by zhangxd68; 02/15/07 05:15 AM.
Re: Water Molecule Occpuancy at a position?
zhangxd68 #13457 02/14/07 10:02 PM
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Did you plot columns 2 and 3? Did any of them look like a g(r)?
Column 2 is g(r) and 3 is basically its integral, from which you can get the "solvation number". Coluimn 1 is not the number of frames, but it is quite easy to figure out what it is.
Since you are not doing a solvent-solvent g(r), but rather a site (your reference point) to solvent g(r) it may be that you should specify iSdist instead of iGdist - I don't remember exactly how the code works for this combination.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Water Molecule Occpuancy at a position?
lennart #13458 02/14/07 11:16 PM
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Thanks Prof. Lennart.

Re: Water Molecule Occpuancy at a position?
lennart #13459 02/14/07 11:48 PM
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To examine water around a peptide or protein site with COOR ANAL, I think you want to use the SITE keyword, and omit the WATER keyword, as in the 3rd g(r) example for water O around backbone HN in corman.doc

If the site is somewhat buried, you may wish to consider exploring the excluded volume options.

COOR HBOND might also be useful to compute how often the site is occupied, and the average lifetime of H-bonds.

Re: Water Molecule Occpuancy at a position?
rmv #13460 02/15/07 03:16 AM
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Thanks Rick.

I figure out the error, I will do this by hand.

Last edited by zhangxd68; 02/15/07 05:20 AM.
Re: Water Molecule Occpuancy at a position?
zhangxd68 #13461 02/15/07 03:46 AM
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Analysing hydrogen bond patterns for:
#donors #acceptors
1st sel: 767 1744
2nd sel: 0 0


For this command to work, both atom selections need to have either donors or acceptors (or both); the 2nd selection is clearly a problem (0 for both), hence the error message.

Your habit of posting cryptic excerpts out of context makes it difficult to say much more.

Re: Water Molecule Occpuancy at a position?
rmv #13462 02/15/07 06:19 AM
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Thanks Prof Lennart and Rick.

Re: Water Molecule Occpuancy at a position?
zhangxd68 #13463 02/15/07 06:58 PM
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COOR HBOND and COOR ANAL do work, and your effort may be better spent learning to use them, rather than "doing it by hand".

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