<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Gromacs Users,<br><br>I am trying to calculate Entropy from Normal Mode Analysis.<br>I minimized the structure to<br>8.41750710592449e-09<br><br>Then I calculated the normal mode (the mdp file is given below). <br><br>But when i try to calculate the Eigenvalues, I get the following warning<br><br><br>One of the lowest 6 eigenvalues has a non-zero value.<br>This could mean that the reference structure was not<br>properly energy minimized.<br>Writing eigenvalues...<br><br>I get only negative eigenvalues.<br><br>Let me also add that I used the same mdp file for minimization changing the integrator to steep, cg and finally to l-bfgs.<br><br>Best,<br>nahren<br><br>-----------------------<br>integrator = nm <br>constraints = none<br>define = -DFLEXIBLE<br>emtol = 0.00000001
<br>emstep = 0.00000001 <br>nsteps = 50000 <br>nstlist = 1 <br>ns_type = grid <br>rlist = 1.5 <br>coulombtype = shift <br>rcoulomb-switch = 1.0 <br>rvdw-switch = 1.0 <br>vdwtype = shift<br>rcoulomb = 1.3<br>rvdw = 1.3</td></tr></table><br>