Mark, hello! I think that there is some error durins saving of my minimization data
As the result of the minimization I've obtained (1) Low-Memory BFGS Minimizer converged to machine precision in 3723 steps, but did not reach the requested Fmax < 0. Potential Energy = 2.08789280994511e+03 Maximum force = 3.01715687185776e-04 on atom 58 Norm of force = 3.09301310600005e-05 So the Fmax is sufficient low But when I've load this data for NMA I've obtained (2) Maximum force: 8.41270e+02 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. So the Fmax is indeed very big for NMA but why it's not the same as in the (1)? This is my script for NMA wich indicate that I've load to NMA suitable data # Steep grompp_d -f minimSTEEP.mdp -c conf_newbox.gro -p topol.top -o minimizedS.tpr mdrun_d -v -deffnm minimizedS # Grad grompp_d -f minimGRAD.mdp -c minimizedS.gro -p topol.top -o minimizedGRAD.tpr mdrun_d -v -deffnm minimizedGRAD # NMA grompp_d -f nma.mdp -c minimizedGRAD.tpr -p topol.top -o fornma.tpr mdrun_d -v -deffnm fornma -mtx nm.mtx Where is the error? James 2011/10/28 Mark Abraham <mark.abra...@anu.edu.au> > On 28/10/2011 2:30 AM, James Starlight wrote: > > That's energy ouptut from minimization with that parametries ( there is > also 1 step of steep minimization before that ) > > integrator = l-bfgs > emtol = 0.001 > emstep = 0.001 ; Energy step size > nsteps = 5000000000 ; Maximum number of (minimization) > steps to perform > > > ; 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 = 1.2 ; Cut-off for making neighbor list (short range > forces) > coulombtype = Shift > rcoulomb = 1.0 > rcoulomb_switch = 0.7 > vdwtype = Shift > rvdw = 1.0 > rvdw_switch = 0.7 > > > Output: > > Low-Memory BFGS Minimizer converged to Fmax < 0.001 in 3646 steps > Potential Energy = 2.28946300988746e+03 > Maximum force = 8.47298141911052e-04 on atom 100 > Norm of force = 3.90346504086500e-04 > > I'm not sure about the succses of that minimization due to the big Epot. > > > > > You look like you are shuffling deck chairs on the Titanic. I suggested > you actually go and visualize your input and output trajectories. Sadly > that doesn't seem to have happened. > > Mark > > -- > 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 >
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