[gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ?? >>> >> I calcualted the average structure from the simulation trajectory. when >> I >> calculate the rmsd of the protein to this average sturture, it is giving >> average rmsd

[gmx-users] rmsd with average structure

Dear Groamcs users, I calcualted the average structure from the simulation trajectory. when I calculate the rmsd of the protein to this average sturture, it is giving average rmsd of 0.16 nm. But, it is not clear for me why the average sturcture is never adapted rmsd near (or equal) to zero. I did

[gmx-users] rmsd fluctuation of the dihedrals

Dear Gromacs users, can some one give me a hint to calculate the " rmsd fluctuation of the dihedrals" to see the angle dynamcis. thanks in advance ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Plea

[gmx-users] dihedral

Dear Gromacs users, Thanks a lot for your input so far. my problem regarding the dihedral angle still suffering me. I need to rotate a bond by certain angle, say from 30 to 150 degrees. i would like to see how the peptide will change its conformation for example CIS to TRANS by the rotation. I tri

[gmx-users] dihedral

Dear all, For example, my peptide is rotating 50 degrees about a bond B-C, out of four bonded atoms A-B-C-D. I want to apply additional force on this dihedral(B-C) during my simulation(only for this particular atoms to make it rotate further till 180 degrees). All the remaining atoms in the pepti

[gmx-users] Re:velocities

Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows.. EM ---> PR(300ps @ 300K) > MD (30ps @ 80K. no postio

[gmx-users] Re: velocities (gmx-users Digest, Vol 29, Issue 60)

Thanks for your answer. I hope I did not catch your points well. So, you mean I can use 'gen_vel = no' for the md runs (MD without position restraints, after the completion of PR run with position restarints) my procedure as follows.. EM ---> PR(300ps @ 300K) > MD (30ps @ 80K. no postio

[gmx-users] velocities

Dear Gromacs Users, I am getting different results for simulations with " gen_vel=yes" and "gen_vel= no". I have generated velocities only for PR MD at 300K. after that I set ' gen_vel= no ' in mdp file. After the position restrained MD , I slowly increased the temparature from 80K , 100K , 200

[gmx-users] Protein out of water box

Dear Gromacs Users, When I use the genbox after editconf , most of the protein is out of water. Even with 'trjconv' after the simulations I cant see any change, as suggested by other gromacs users. Pls some one give me an idea... thank you very much! best regards Gajula