p.s. How big is this negative value? Ran Friedman wrote: > 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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