Hi all, I am trying to repeat the solvation energy calculation as done by Villa and MArk in (A. Villa and A. E. Mark Calculation of the free energy of solvation for neutral analogues of amino acid side chains. J. Comput. Chem, 23 (2002) 548-553.).
I am not sure about the way I am doing my in vacuum simulation. attached is my mdp: integrator = sd . . . ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = berendsen ; Groups to couple separately, time constant (ps) and reference temperature (K) tc-grps = system tau-t = 0.1 ref-t = 298 ; Pressure coupling Pcoupl = no ; Generate velocites is on at 290K - do not get velocity from gro file. gen_vel = yes gen_temp = 290 ld_seed = 12 ; Free energy control stuff free-energy = yes init-lambda = 0 ; Topology A (lambda=0) to topology B (lambda=1). delta-lambda = 0 sc-alpha = 0.5 ; soft core potantial sc-power = 1 sc-sigma = 0.3 . . . ; Center of mass control nstcomm = 10000 ; Periodic boundary conditions pbc = xyz comm_mode = angular My question are: 1. Is there any meaning or temperature when one does SD in vacuum? 2. Does my lambda parameters ore fine? 3. Does the way I treat the center of mass motions is OK? Best, Itamar --- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: [email protected] ============================================
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