[gmx-users] Normal Mode Analysis

[Mark Abraham]

On 24/10/2011 3:12 AM, James Starlight wrote:
> 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=nm 
> I'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?

That .mdp file did not produce that output.

Mark