Well, a search on this list would have yielded a longish message I
wrote, explaining how this works:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-December/077005.html
(but look also at other messages in that thread) where this is also expressed:
"It's the user's responsibili
On Mon, Mar 23, 2015 at 5:33 AM, Alex wrote:
> I specifically want to reparameterize the bond, angle, and the dihedral
> constants with something that I know to be at least somewhat representative
> of graphene and isn't something from oplsaa, which comes from an entirely
> different paradigm.
>
On Fri, Jan 16, 2015 at 2:56 PM, mah maz wrote:
> These potential energies are the average ones, how can I get the final
> potential of the system?
In the log file you get instantaneous values for all types of
calculated energies. You can also get it with g_energy, but you'd have
to read a bit mo
On Dec 10, 2014 10:21 PM, "Jackson Chief Elk" wrote:
>
> Hi,
> I am building my own routine to use the Gromacs API to do MS-EVB. I need
to treat O-H bonds of 1 hydronium ion with a Morse Potential. How can I
specify in the *.mdp file, to just describe bonding in hydronium using this
potential?
On Mon, May 12, 2014 at 12:49 PM, Hardy, Adam wrote:
> If gen-pairs is set to yes, does it overwrite parameters given in the itp
> file? This way I would not have to go through and explicitly list the
> "normal" 1-4 interaction parameters in the itp file.
I have tried to explain how the exclusi
On Fri, Nov 22, 2013 at 4:27 PM, Mark Abraham wrote:
> Anybody wanting to add functionality to trjconv will need to offer me a
> raise along with it ;-)
The functionality should never be added to trjconv, independent of
your raise :) trjconv does trajectory (and structure files along the
way) con
