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Joined: Jul 2005
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krishna Offline OP
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Hi,

I recently defined alcohol topologies using existing Glycerylphosphorylcholine topology. While running MD with GBSW solvation, I noticed alcohols forming hydrogen bonds with themselves. For eg: In Glycerol (CH2-OH -- CH-OH -- CH2-OH), the first -OH hydrogen bonds with oxygen of second -OH. Is this possible with explicit solvation ? Have anyone else noticed this kind of hydrogen bonding ? I used a distance cutoff of 2.4 A for defining hydrogen bonds.

Thanks

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rmv Offline
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Most implicit solvent models seem to be tuned to protein behavior, and do a rather poor job with molecules (ethers, polyols, carbohydrates) whose solution structure depends on explicit solvent interaction.


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