These are the all commands to do iteration: After generating topology - concatenate the protein and bilayer structure files: #cat dimer-newbox.gro popc-whole.gro > system.gro ( Remove unnecessary lines and update the second line of the coordinate file (total number of atoms) accordingly )
- Use a very strong position-restraining force on protein heavy atoms to ensure that the position of the protein does not change during EM : Adding these lines to topology file: ; Strong position restraints for InflateGRO #include "topol_Protein_A.itp" #ifdef POSRE #include "strong_posre.itp" #endif #include "topol_Protein_B.itp" #ifdef POSRE #include "strong_posre.itp" #endif - Now, generate this new position restraint file using genrestr: #genrestr -f dimer-newbox.gro -o strong_posre.itp -fc 100000 100000 100000 - In the .mdp file used for the minimizations, add a line "define = -DSTRONG_POSRES" to make use of these new position restraints. - Scale the lipid positions by a factor of 4: #perl inflategro.pl system.gro 6 POPC 14 system_inflated.gro 5 area.dat Updating the .top file and adding POPC 238 to it. ITERATION 1. Energy minimization with restrained protein #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr #mdrun -deffnm em Steepest Descents converged to Fmax < 1000 in 137 steps Steepest Descents converged to Fmax < 100 in 4998 steps Potential Energy = 1.1410846e+04 Maximum force = 9.4570084e+01 on atom 8800 Norm of force = 3.2672191e+00 scale down the lipids by a factor of 0.95 #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat 2. #grompp -f minim.mdp -c em_shrink1.gro -p topol.top -o em_shrink1.tpr # perl inflategro.pl em_shrink1.gro 0.95 POPC 0 em_shrink2.gro 5 area_shrink2.dat 3. # grompp -f minim.mdp -c em_shrink2.gro -p topol.top -o em_shrink2.tpr # perl inflategro.pl em_shrink2.gro 0.95 POPC 0 em_shrink3.gro 5 area_shrink3.dat . . . . Then, after 32 iterations, the APL reaches the value of 10% higher than the experimental value. So, I use the last gro file em_shrink32.gro as the initial configuration to solvate and next steps. But when I check the overlaps in em_shrink32.gro, there are many improper overlaps and acyl penetration to the protein, disgusting! Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Monday, June 10, 2013 11:12 PM Subject: Re: [gmx-users] restraints on water oxygen atoms On 6/10/13 12:24 PM, Shima Arasteh wrote: > Would you please tell me which initial deletion radius? > It would be easier for you to provide the exact command(s) you're using. Maybe you've posted this information before, but this thread (or at least, related topics) has gone on for a very long time and maybe I'm forgetting. > And do you mean a smaller scale up factor ( for example 0.90 ) by saying > shrink more slowly? > A larger shrinking factor, e.g. 0.95 or 0.97, will shrink more slowly. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
