Hi, I have a couple of questions about FE calculations. I am following the tutorial by Dill group for calculating the solvation FE of a non-standard residue.
1) Trivial questions first: It is advised to use PME with opls, is it possible to use PME in vacuo? As far as I know PME depends on periodicity, which is shut-off in vacuo. 2) Should I extract dv/dl values from my .edr file to get dG? Can I use dgdl.xvg file? It is trivial but I am confused about this procedure. 3) I have smooth simulations when init_lambda < 1. But When I get to lambda =1, I sometimes get enormously high energy values (in a fluctuating manner) for my system. What could be the problem? 4) As you see in the mdp file, I used sc_alpha = 0. Otherwise, my system gives out error. Is it bad to use sc_alpha =0? 5) Should I use FE parameters in my energy minimization simulations? Normally, I used my minimized lambda=0 structure as input for other lambda simulations without doing further EM. I also tried to include lambda values in my EM files and I got junk results (.gro files and energy values). and this is my mdp file for in vacuo MD: title = MD in vacuo cpp = /lib/cpp include = -I/../EM/ integrator = sd tinit = 0 dt = 0.001 nsteps = 2500000 ; number of steps for center of mass motion removal = nstcomm = 100 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 0 xtc-precision = 1000 ;xtc_grps = Protein nstlist = 10 ns_type = grid ;pbc = xyz rlist = 1.4 coulombtype = Shift rcoulomb = 1.2 rcoulomb_switch = 1.0 epsilon-r = 1.0 vdw-type = Shift rvdw = 1.2 rvdw_switch = 1.0 DispCorr = EnerPres ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t = 1.0 ref_t = 300 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = No tau_p = 0.5 compressibility = 4.5e-05 ref_p = 1.0 ; Free energy control stuff free_energy = yes init_lambda = 1.0 delta_lambda = 0 sc_alpha =0.0 ;sc-power =1.0 sc-sigma = 0.3 ; GENERATE VELOCITIES FOR STARTUP RUN = meaningful only with md integrator gen_vel = yes gen_temp = 300 gen_seed = -1 thanks in advance. Murat CETINKAYA, M.Sc. BioNanoMaterials Group, Dept. of Engr. Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 office: (814) 863 9967 web: www.personal.psu.edu/muc176 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
