hi,
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
; NEIGHBORSEARCHING PARAMETERS
; 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
; OPTIONS FOR ELECTROSTATICS AND VDW
; 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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