I find getting a system minimised is often quite tricky. There's a variety of things that can be fiddled with, using cg with various intervals between steps of steepest descent, running a few steps of md (say, 10 to 100) after minimisation and then minimising again, randomly perturbing the coordinates of the problem atoms manually in the .gro file and retrying, stuff like that. Make sure there's no obvious bad contacts in the structure first, my personal nemesis seems to be lipid tails stuck through tryptophan rings...
--- Pradip Kumar Biswas <[EMAIL PROTECTED]> wrote: > Hi, > > What is your 'emstep' value in your mdp file? Could > you try to rerun > your system with a low emstep; say with emstep = > 0.00001 > or else? > > pb. > > > On Jul 18, 2006, at 1:13 AM, Srivastava, Dhiraj > (UMC-Student) wrote: > > > Hi all > > > > when i am trying to minimize my structure, i > am getting > > following error. > > > > Stepsize too small, or no change in energy. > > Converged to machine precision, > > but not to the requested precision Fmax < 1000 > > > > Double precision normally gives you higher > accuracy. > > > > writing lowest energy coordinates. > > > > Back Off! I just backed up prodh_em.trr to > ./#prodh_em.trr.2# > > > > Back Off! I just backed up prodh_wb.pdb to > ./#prodh_wb.pdb.4# > > > > Steepest Descents converged to machine precision > in 45 steps, > > but did not reach the requested Fmax < 1000. > > Potential Energy = -1.8373166e+06 > > Maximum force = 1.5158329e+04 on atom 519 > > Norm of force = 3.1759754e+04 > > > > > > i have tried the conjugated gradient, constraint > none and also > > included flexible water but still i am getting the > same error. > > > > what should i do to solve this problem? > > > > Thanks in advance for help. > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the > list. Use the > > www interface or send it to > [EMAIL PROTECTED] > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > Pradip K. Biswas, PhD. > Research Associate, Department of Chemistry; > Cleveland State University, Ohio-44115 > Phone: 1-216-875-9723 > http://comppsi.csuohio.edu/groups/people/biswas.html > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the > list. Use the > www interface or send it to > [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
