[gmx-developers] Implicit solvation model

Vibin R vinu at btc.iitb.ac.in
Thu Feb 6 10:39:04 CET 2003


There is a subroutine in Gromacs (g_sas) for calculating SASA for protein.
I wonder if there is any possibility of incorporating this term in force
field to effect implicit solvation? This can be achieved by
SASA with mean solvation parameters of atom types. The method has already
been implemented by W. F. van Gunsteren (Ref. JMB 1996, 256, 939-948).
Caflisch implimented a similar method in CHARMM as an implicit solvent
model for MD (Ref. PROTEINS: Structure Function and Genetics 2002, 46;

Recently Oleg et al has reported a much better procedure for calculating
SASA. (Ref. J Comput. Chem. 2002: 23; 600-609).

Is there any possibility of integrating mean solvation parameter in the
force field of Gromacs?

 Vibin Ramakrishnan         	
 De novo design lab
 School of Biosciences and Bioengineering
 IIT Bombay                          	
 Ph: 91-22-57624780,57624168
 Hostel 8 ; Room No 183    

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