[gmx-users] problem normal mode analysis

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Fri Feb 12 15:16:10 CET 2010

   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 
where have i gone wrong?
Any suggestion will be of great help.
Thanks in advance.
Sarbani Chattopadhyay
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100212/aa0ffe8e/attachment.html>

More information about the gromacs.org_gmx-users mailing list