<div style="font-family: 'Times New Roman'; font-size: 16px;"><br /><br /><span>On 02/13/10, <b class="name">sarbani chattopadhyay </b> <sarbani_c84@rediffmail.com> wrote:</span><blockquote cite="mid:20100212141610.2840.qmail@f5mail-237-205.rediffmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">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?</div></blockquote><br _moz_dirty="" />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.<br _moz_dirty="" /><br _moz_dirty="" />Mark<br _moz_dirty="" /><div _moz_dirty="" class="mimepart text html"><table border="0" cellpadding="0" cellspacing="0" height="57" style="font-family: Verdana; font-size: 11px; line-height: 15px;" width="644"><tbody><tr><td><br _moz_dirty="" type="_moz" /></td></tr></tbody></table></div></div>