Dear Mark I explain you what I want to ask . I give you a detail of my processing - * step for packing lipid around protein- 1. concatanation of protein and lipid bilayer in proper orientation- I did. 2.Inflate the bilayer by using inflategro script with scaling factor 4 and cutoff 14- I did . there is 8 lipid removed in this process and a/c to that I have update my topology file . 3. Energy minimisation by applying strong position restrain on protein the force constant=100000
problem occur here is- Step= 344, Dmax= 1.8e-05 nm, Epot= 4.29315e+06 Fmax= 1.02525e+05, atom= 4615 Step= 349, Dmax= 1.4e-06 nm, Epot= 4.29315e+06 Fmax= 9.86524e+04, atom= 4615 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. writing lowest energy coordinates. Steepest Descents converged to machine precision in 350 steps, but did not reach the requested Fmax < 1000. Potential Energy = 4.2931510e+06 Maximum force = 1.0252509e+05 on atom 4615 Norm of force = 1.3668822e+03 my em.mdp file- cpp = /usr/bin/cpp define = -DPOSRES constraints = none integrator = steep nsteps = 10000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no comm-mode = Linear pbc = XYZ my topology file is like this- ; Include forcefield parameters #include "ffG53a6_lipid.itp" #include "topol_A.itp" #ifdef POSRES #include "posre_A.itp #include "topol_B.itp #ifdef POSRES #include "posre_B.itp #endif ; Include DMPC chain topology #include "dmpc.itp" [ system ] ; Name Protein in DMPC bilayer [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 DMPC 120 my question- 1. probable reason of steepest descent converged to macine precision but did not reach the requested Fmax < 1000. 2.The even after applying strong position restrain on protein the protein structure being disturbed. If u can make help for me . I will appreciate you. Thanks Nitu sharma
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
