Dear Gromacs Users,
I am trying to calculate Entropy from Normal Mode Analysis.
I minimized the structure to
8.41750710592449e-09
Then I calculated the normal mode (the mdp file is given below).
But when i try to calculate the Eigenvalues, I get the following warning
One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.
Writing eigenvalues...
I get only negative eigenvalues.
Let me also add that I used the same mdp file for minimization changing the
integrator to steep, cg and finally to l-bfgs.
Best,
nahren
-----------------------
integrator = nm
constraints = none
define = -DFLEXIBLE
emtol = 0.00000001
emstep = 0.00000001
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.5
coulombtype = shift
rcoulomb-switch = 1.0
rvdw-switch = 1.0
vdwtype = shift
rcoulomb = 1.3
rvdw = 1.3
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