Hi, When doing EM it is not a good idea to use restrains/constraints when doing EM.
Try minimize without it. Best, Itamar --- "Prediction is very difficult, especially about the future" - Niels Bohr =========================================== | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The University of Queensland | St. Lucia Campus, Brisbane, QLD 4067 | Australia | | Tel: +61 7 3365 9922 | Fax: +61 7 3365 3872 | E-mail: [EMAIL PROTECTED] | Web page: http://www.uq.edu.au/~uqikass/ | Personal web page: http://thekassfamily.blogspot.com/ ============================================ Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland ----- Original Message ----- From: Mark Abraham <[EMAIL PROTECTED]> Date: Friday, May 18, 2007 11:06 am Subject: Re: [gmx-users] energy minimization - double precision > Pradeep Kota wrote: > > Dear users, > > I'm trying to minimize the energy of a protein in vacuum. I have > > restrained the backbone with posre.itp generated using genpr. > when i try > > to minimize the energy of this protein using single precision > grompp > > followed by an mdrun, it does not converge even after 600 steps > and > > returns saying that it could not get to the requested minimum > energy, > > and suggested that i use double precision for the same. so, i > compiled > > gromacs with double precision and tried the same and i get the > > following. Could you help me solve this? > > Try a visual inspection of your structure before and after the > single-precision minimization and look for sources of problems. You > don't actually need convergence of minimization before an > equilibration > mdrun is a reasonable thing to try. Double precision minimization > is > only something you care about before (say) a normal-mode analysis. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting!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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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