Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with Money
Non-cutoff electrostatics used, forcing full Hessian format. Allocating Hessian memory... starting normal mode calculation 'Pure Water' 648 steps. Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized. Finished step 648 out of 648 Writing Hessian... gcq#258: "In the End Science Comes Down to Praying" (P. v.d. Berg) g_nmeig_d -f nm.mtx -s water.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr Reading file water.tpr, VERSION 4.0.4 (double precision) Reading file water.tpr, VERSION 4.0.4 (double precision) Reading double precision matrix generated by Gromacs VERSION 4.0.4 Full matrix storage format, nrow=1944, ncols=1944 Diagonalizing to find vectors 1 through 50... 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... Writing eigenfrequencies - negative eigenvalues will be set to zero. Writing average structure & eigenvectors 1--50 to eigenvec.trr gcq#132: "Shit Happens" (Pulp Fiction) The eigenfreq is 0 which is the problem The .mdp file used was; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = define = -DFLEXIBLE constraints = none integrator = nm nsteps = 10000 ; ; Energy minimizing stuff ; emtol = 0.01 emstep = 0.01 coulombtype = PME nstcomm = 1 ns_type = grid rlist = 0.9 rcoulomb = 0.9 rvdw = 0.9 Tcoupl = no Pcoupl = no gen_vel = no
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