[gmx-users] query regarding normal mode analysis

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Thu Mar 18 10:24:30 CET 2010

  I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.00000e-03.
               Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off" for electrostatics and Van der Waals interaction with rvdw and rcuolomb=0.

define                   = -DFLEXIBLE
constraints              = none
integrator               = l-bfgs
tinit                    = 0
nsteps                   = 15000
nbfgscorr                = 50
emtol                    = .001
emstep                   = 0.1
gen_vel                  = yes
gen-temp                 = 300
nstcomm                  =  1
; nblist update frequency
nstlist                  = 0
; ns algorithm (simple or grid)
ns-type                  = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = no
; nblist cut-off
rlist                    = 0
domain-decomposition     = no
; Method for doing electrostatics
coulombtype              = Cut-Off
rcoulomb-switch          = 0
rcoulomb                 = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r                = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 0

The Fmax went down to  
Maximum force     =  9.67927896882578e-07 on atom 3271, after doing the energy minimization with the above parameters twice.

Then I used the same parameters, (while only changing the "integrator=nm") and did the normal mode analysis. 
The maximum force as calculated before the NMA was
Maximum force: 9.67928e-07.

Thus the Fmax as calculated at the end of the energy minimization and at the start of the NMA was the same.
But while going through the  gromacs manual and the user mailing list archives, I have seen that the it is suggested that the van der Waals and Coulomb interactions should be calculated as

switched Coulomb & van der Waals interactions; cutoffs e.g. at 1.0 nm, switched from 0.8 nm (or shifted from 0 nm).
rlist at 1.2 to 1.3

Changing the parameters in nm.mdp file gives the following message:Maximum force: 2.50866e+02 Maximum force probably not small enough to ensure that you are in anenergy well. Be aware that negative eigenvalues may occur when theresulting matrix is diagonalized.

If I use these parameters in the energy minimization step the Fmax does not go down. Have I done the process correctly, or should I try again to reduce the Fmax in energy minimization step using switched cuolomb and van der waals interactions and then do NMA.

Any suggestion will be of great help.
Thanking You,
Sarbani Chattopadhyay 

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