On 24/10/2011 6:56 PM, James Starlight wrote:
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?
These are particular to the force field involved, not the software.
Please consult the appropriate literature, and see what others have used
for similar work.
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?
Smaller EM steps might do something.
Finally I've forced with the diffuculty of the analysing of my data by
the g_anaeig
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 ?
We can't tell from this information.
Mark
Thanks,
James
2011/10/23 James Starlight <jmsstarli...@gmail.com
<mailto:jmsstarli...@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=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?
James
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