As the consequence I've done my NMA calculations without of any constraints :)
integrator = nm ; Normal Mode Analysis constraints = none but I'm not sure if this could be valid because I didnt found any literature of such NMA in Gromacs. Could someone provide me with the appropriate cut-offs for the NMA in gromacs? By the way before this NMA I've done 2 energy minimization calculations first by Steepest algorithm (emtool= 1000) and then by CG ( emtool=10) but resulting force was still not small enought (8.92766e+02). How I can futher minimize my structurere? Finally I've forced with the diffuculty of the analysing of my data by the g_anaeig E,g I want to obtain fluctuations of some atoms from my eigenvectors g_anaeig -s fornma22.tpr -v eigenvec.trr -eig eigenval2.xvg -rmsf -first -1 1 0 I've obtained a .xvg file fith the fluctuations along 1st mode but during opening that file by xgrace I've obtain some input error. Whats I've done wrong ? Thanks, James 2011/10/23 James Starlight <[email protected]> > I want to come back to the question of the NMA in the Gromacs :) > > I've found in manual possible algorithms of this analysis- I must > calculate Hessian matrix via Md-run and then calculate modes with g_nmens > program > > > 1- I've performed CG minimization of my initianl structure > > 2- I've loadet to the gromp .tpr file of my minimized structure > > 3- I've used mdrun and obtain error > Fatal error: > Constraints present with Normal Mode Analysis, this combination is not > supported > > So I suppose that the problem with my .mdp file wich consist of the > parametres for the NMA of Lyzosyme in water :) > > integrator = nm ; Normal Mode Analysis > > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long > range forces > ns_type = grid ; Method to determine neighbor list (simple, > grid) > rlist = 1.0 ; Cut-off for making neighbor list (short range > forces) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.0 ; Short-range electrostatic cut-off > rvdw = 1.0 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > > How I should edit this configure file for my NMA? > If I edit the above parametries for rvdw etc in accardance to the > http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis?highlight=nmI've > obtained error that > > ERROR 1 [file nma.mdp]: > With coulombtype = PME, rcoulomb must be equal to rlist > If you want optimal energy conservation or exact integration use > PME-Switch > > > ERROR 2 [file nma.mdp]: > With vdwtype = Cut-off, rvdw must be >= rlist > > What are the most suitable coulombtype for the NMA and combination of the > other options? > > > James > > >
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