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