Hi, I guess posting the whole set of commands you used and mdp file for NMA can help. Best, Ran
sarbani chattopadhyay wrote: > hi, > I want to do a normal mode analysis on a small peptide. > I had complied gromacs in double precision and energy minimized the > structure in vacuum, > using steepest descent followed by conjugate gradient method. the log > file of conjugate > gradient method reads > Polak-Ribiere Conjugate Gradients converged to Fmax < 0.0001 in 1023 steps > Potential Energy = -1.95899271351756e+02 > Maximum force = 9.50250289517625e-05 on atom 48 > Norm of force = 3.82317661305055e-05 > > but when i try to run mdrun_d ( for normal mode analysis) , it shows > Maximum force: 2.05241e+02 > 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 > > I had made grompp_d read the trajectory file of "cg energy > minimization" by using the -t > flag. > where have i gone wrong? > Any suggestion will be of great help. > Thanks in advance. > Sarbani Chattopadhyay > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline....@middle?> > >
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