On Wed, Apr 10, 2013 at 1:42 AM, James Starlight <jmsstarli...@gmail.com>wrote:
> Mark, > > > first of all I think that something wrong in amber and charm simulations > because of some fluctuations of the box x-y-z dims during simulation > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Box-X 9.32108 0.0068 0.0360834 0.0289953 (nm) > Box-Y 8.89245 0.0064 0.0344241 0.0276619 (nm) > Box-Z 9.07051 0.013 0.0702945 -0.0525563 (nm) > > > so due to decreasing of the box dims the overal conformational behaviour of > the system is very 'straitjacketed' - its likely my protein placed in the > compact crystal environment preventing its dynamics. > > I don't see any basis for such claims. You have relatively minor changes in all dimensions, indicating the box is fairly stable. Depending on how you constructed the initial configuration, some relaxation in any dimension is perfectly reasonable. CHARMM is likely the most widely used force field for membranes; I see no reason to say that using it causes any weird behavior. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
