[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Mon Oct 24 09:56:48 CEST 2011

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
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 ?


2011/10/23 James Starlight <jmsstarlight at gmail.com>

> 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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