[gmx-users] Protein is not at the centre of octahedron box

Dear All, I am doing a simulation for ligand-enzyme complex in a octahedron box. I have mentioned -c with editconf, but after energy minimization the protein is placed at the top of the box. Could you please suggest me how could I keep the protein at the centre of the octahedron box? Here are

[gmx-users] RMS deviation after position restraint dynamics

Dear All, I am running position restraint dynamics to restrain the atom positions of the protein to restrict their movement in the simulation. Then, how could there be any RMS deviation for the protein before and after the position restraint dynamics run? (Although the deviation is very little)

[gmx-users] Problem with box-type after the extension of simulation

see the result after using trajconv (additionally some part of the protein is out of the box). I do not have any clue how the box type has been changed or where could I go wrong. Please comment. Thank you, Cheers, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd

[gmx-users] Analysis of a simulation

. It would be a great help if you could kindly give some sample commands for these analysis. Sorry for lots of questions. Thank You. Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 4

[gmx-users] Position restrained dynamics crash

= 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank You, Regards, Sukesh. -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park'

[gmx-users] Dynamic cross correlation map

ovar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/

[gmx-users] Dynamics cross correlation map

ovar.dat Waiting for your input. Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

[gmx-users] Dynamics cross correlation map

n and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain

[gmx-users] Unstable model : need suggesstion

Dear All, I have done a simulation (in water) of PfPBGD model protein for 500 ps. But when I compared the secondary structure of my native protein structure vs structure after simulation. I observed that lot of unfolding is happening after simulation. So, my queries are: 1> Is there any way I can i