On 02/13/10, sarbani chattopadhyay <[email protected]> wrote:
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?
You've gone wrong in not copying and pasting your series of command lines and quoting your GROMACS version. There would seem to be a mismatch between what you think you're doing and what GROMACS knows you've asked for. Make sure you check the grompp output for warnings, etc. too.
Mark
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