[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Sun Oct 23 18:12:40 CEST 2011

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

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,
rlist        = 1.0        ; Cut-off for making neighbor list (short range
coulombtype    = PME        ; Treatment of long range electrostatic
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
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

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?

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