[gmx-users] problem normal mode analysis

[sarbani chattopadhyay]

hi,
   I want to do a normal mode analysis on a small peptide.
I had complied gromacs in double precision and energy minimized the structure in vacuum, 
using steepest descent followed by conjugate gradient method. the log file of conjugate 
gradient method reads 
Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 1023 steps
Potential Energy  = -1.95899271351756e+02
Maximum force     =  9.50250289517625e-05 on atom 48
Norm of force     =  3.82317661305055e-05

but when i try to run mdrun_d ( for normal mode analysis) , it shows
Maximum force: 2.05241e+02
Maximum force probably not small enough to ensure that you are in an
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized

I had made grompp_d read the trajectory file of "cg energy  minimization" by using the -t 
flag.
where have i gone wrong?
Any suggestion will be of great help.
Thanks in advance.
Sarbani Chattopadhyay
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