Ni Hao, You don't give too much information here. What exactly are you doing? What are the commands? What's the difference between the first and the second pass of EM? One thing to check is whether the output/input file has a correct box definition.
Cheers, Tsjerk 2009/11/30 HAO JIANG <hj.pub...@gmail.com>: > Hi, > > I got a problem with the output structure files (gro/trr/xtc) generated by > the energy minimization with GROMACS 4. That is, when I used the generated > structure as the input for further minimizations or MD simulations, I got > very large potential energy and forces at step 0, as if the structure had > not been optimized at all. On the other hand, there is no problem when > the input structure is taken from a previous MD run, and I got the expected > potential at step 0. There is no problem, too, if I use GROMACS 3 to do the > minimization. > > Any help is greatly appreciated! > > Hao Jiang > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
