[gmx-users] alkane-aqueous interfacial simulations

[Jayant James Jayasundar]

Dear gmx_users,
I am simulating a protein in hexane-aqueous, octane-aqueous and decane-aqueous interfaces to understand the relation between activity and interface hydrophobicity. I built the 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. 
The results of my simulations conducted over 5ns showed an expected conformational change in a particular mobile loop of the protein that covers the active site. The deviates are 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 also verified by essential dynamics).

Question

Would Gromacs differentiate between a C6, C8, C10 based on their back bone lengths so as to identify which is more hydrophobic interface.?
 
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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