Quoting chaiann ng <andy810915.hotmail.com>:
> I am trying to create a cyclohexane box for my simulation. I am using the
> input for under the folder "solvent" in the amber directory and also the
> input file from the web. I am getting density of less than 0.4 at 300K after
> 50ps MD, which is the initial density when i solvate my cyclohexane (chair
> conformation) with a box of cyclohexane. Can anyone help? Attached is the
> PDB file of the cyclohexane and prepin file. Thanks.
When you calculated the RESP charges for the cyclohexane, did you check the RRMS
of the fit ? For me, it is closed to ONE !!! My understanding is that the RESP
charges centered on the cyclohexane atoms are verrrry bad, and cannot reproduce
the MEP computed by QM...
See
http://www3.interscience.wiley.com/cgi-bin/abstract/109583172/ABSTRACT
I wonder what would give a box of cyclohexane in these conditions.
Regards, Francois
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Received on Thu Nov 03 2005 - 08:53:00 PST
