[gmx-users] problems with normal mode analysis

[Kristina Woods]

Hello,

I have done a energy minimization of my DNA + solvent system for a
normal mode analysis.  The lowest energy coordinates that I received
after the minimization were the following:

writing lowest energy coordinates.

Polak-Ribiere Conjugate Gradients converged to machine precision in -1 steps,
but did not reach the requested Fmax < 1e-06.
Potential Energy  = -2.41611379206922e+04
Maximum force     =  5.16729332737359e-04 on atom 53
Norm of force     =  3.89188453193799e-05

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But when I try to perform the normal mode analysis the Fmax value
increases significantly:

Reading file nm_drop.tpr, VERSION 3.2.1 (double precision)
starting nmrun 'DNA'
939 steps.

Maximum force: 2.52765e+03
Maximum force probably not small enough to ensure that you are in a 
energy well. Be aware that negative eigenvalues may occur when the
resulting matrix is diagonalized.

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I believe I am using the lowest energy coordinates from the prior
minimization (i.e. the -t option in grompp with the energy minimized
.trr file)...but I still get a huge maximum force value in the normal
mode analysis.

Has anyone else experienced this?  Does anyone have any suggestions?

Thank you,

Kristina :)