[gmx-users] Assigning protonation states using Amber ff

needed to use Amber. Any advice on this would be appreciated! Thanks in advance, Zoe Hall Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Adding OPLS-UA forcefield

Dear users, How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 4.5.3? Thanks in advance, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] Re: Simluations in vacuum - energy increase

the simulations - I don't really understand this. Thanks, Zoe On 2011-04-30 14.17, Zoe Hall wrote: > Gmx-users, > > I am trying to carry out a simulation of lysozyme in vacuo using the > OPLS-AA forcefield. After energy minimisation, the protein is run for > 10ps with po

[gmx-users] Simulations in vacuo - energy increase

= yes ; gen_temp = 300.0 gen_seed = -1 constraints = hbonds constraint-algorithm = LINCS lincs_order = 4 Thanks, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- gmx-users mailing listgmx

[gmx-users] Simulations in vacuo

, what is the appropriate choice for "coulombtype" and other electrostatic parameters for vacuum simulations. I have set "epsilon_r" to 2, as this seems to be an accepted value for proteins but if anyone has comments on this, I would appreciate it. Thanks very much, Zoe Zo