[gmx-users] alkane interfaces

[Jayant James Jayasundar]

Hi!
I am simulating a protein in hexane-aqueous, octane-aqueous and decane-aqueous interfaces to understand the relation between activity and hydrophobicity. I built C6 & C8 molecules by means of PRODRG (decane’s coordinates are already in Gromacs). The protein was solvated in an aqueous environment containing 5777 aqueous molecules. In this box sufficient number of alkanes were added such that they form a spherical interface. 
My results of simulations conducted over 5ns shows that the conformational change in a particular mobile loop that moves during activation is in the order, hexane > octane > Decane( least in C6- aqueous interface, moderate in C8-aqueous interface greatest in decane-aqueous interface in terms of deviation measured in Angstroms).

Questions
1.Would Gromacs differentiate between a C6, C8, C10 based on their back bone lengths so as to identify which is more hydrophobic?
2. Is the phenomenon of studying interface hydrophobicity by increasing alkane chain length valid using GROMACS.
Thanks
Jayant




Jayasundar Jayant James
Research scholar
Centre for Biotechnology,Anna University,
Chennai - 600 025.INDIA .Ph 2350772(Office)
www.chick.com/reading/tracts/0096/0096_01.asp) 
Residence -24935864, cell-9841042164.
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