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Hi,<br>
I guess posting the whole set of commands you used and mdp file for NMA
can help.<br>
Best,<br>
Ran<br>
<br>
sarbani chattopadhyay wrote:
<blockquote
cite="mid20100212141610.2840.qmail@f5mail-237-205.rediffmail.com"
type="cite">hi,<br>
I want to do a normal mode analysis on a small peptide.<br>
I had complied gromacs in double precision and energy minimized the
structure in vacuum, <br>
using steepest descent followed by conjugate gradient method. the log
file of conjugate <br>
gradient method reads <br>
Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 1023
steps<br>
Potential Energy = -1.95899271351756e+02<br>
Maximum force = 9.50250289517625e-05 on atom 48<br>
Norm of force = 3.82317661305055e-05<br>
<br>
but when i try to run mdrun_d ( for normal mode analysis) , it shows<br>
Maximum force: 2.05241e+02<br>
Maximum force probably not small enough to ensure that you are in an<br>
energy well. Be aware that negative eigenvalues may occur when the<br>
resulting matrix is diagonalized<br>
<br>
I had made grompp_d read the trajectory file of "cg energy
minimization" by using the -t <br>
flag.<br>
where have i gone wrong?<br>
Any suggestion will be of great help.<br>
Thanks in advance.<br>
Sarbani Chattopadhyay<br>
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