Hi, Can you post the exact commands you used for EM and NMA?
Ran nahren manuel wrote: > Dear Gromacs Users, > > I am trying to calculate Entropy from Normal Mode Analysis. > I minimized the structure to > 8.41750710592449e-09 > > Then I calculated the normal mode (the mdp file is given below). > > But when i try to calculate the Eigenvalues, I get the following warning > > > One of the lowest 6 eigenvalues has a non-zero value. > This could mean that the reference structure was not > properly energy minimized. > Writing eigenvalues... > > I get only negative eigenvalues. > > Let me also add that I used the same mdp file for minimization > changing the integrator to steep, cg and finally to l-bfgs. > > Best, > nahren > > ----------------------- > integrator = nm > constraints = none > define = -DFLEXIBLE > emtol = 0.00000001 > emstep = 0.00000001 > nsteps = 50000 > nstlist = 1 > ns_type = grid > rlist = 1.5 > coulombtype = shift > rcoulomb-switch = 1.0 > rvdw-switch = 1.0 > vdwtype = shift > rcoulomb = 1.3 > rvdw = 1.3 > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman ------------------------------------------------------
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