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
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