[gmx-users] Entropy from NMA

nahren manuel meetnahren at yahoo.com
Wed Jul 28 11:37:15 CEST 2010

Dear Gromacs Users,

I am trying to calculate Entropy from Normal Mode Analysis.
I minimized the structure to

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.


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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