Dear all,
Those of you who read the paper will realize that we do acknowledge Tsjerk,
and keep doing so on the web pages of the material, but there are reasons
we considered sufficient to justify the author listing on the paper.
However, since Tsjerk knows me and the other authors (them actually
2ubYrFg>.
Here's the pastebin for the grompp command. <http://pastebin.com/J22XMt7N>
Let me know what I can do to help you debug, or if I'm doing something
wrong.
Cheers and thanks,
João
2015-05-04 21:43 GMT+02:00 João Rodrigues :
> Hi all,
>
> I am trying to setup
Hi all,
I am trying to setup a simulation of a peptide with neutral termini, using
the CHARMM36 port from the MacKerell lab. While pdb2gmx works well, grompp
fails with several erros about missing parameters, e.g.:
ERROR 1 [file topol.top, line 1225]:
No default U-B types
...
ERROR 4 [file to
Checked. Fixed.
Thanks again!
João
2014-03-14 14:03 GMT+01:00 João Rodrigues :
> Hi Carsten,
>
> Thanks for the fix!
>
> Will run it today and get back to you with the results.
>
> Cheers,
>
> João
>
>
> 2014-03-14 12:32 GMT+01:00 Carsten Kutzner :
>
>
gt;
> Thanks,
> Carsten
>
>
>
> On 13 Mar 2014, at 18:27, João Rodrigues wrote:
>
> > Hi Carsten,
> >
> > Thanks for the reply and for the info on the rlist modification.
> >
> > I created the bug report - http://redmine.gromacs.org/issues/1460
gt; Dear João,
>
> On 13 Mar 2014, at 14:38, João Rodrigues wrote:
>
> > Hi all,
> >
> > I've been playing with g_tune_pme (neat tool!) for the last couple of
> days.
> > If I understood correctly, it can also be used to iterate over different
> > r
Hi all,
I've been playing with g_tune_pme (neat tool!) for the last couple of days.
If I understood correctly, it can also be used to iterate over different
rcoulomb values using the -rmin and -rmax options. Using the Verlet scheme
requires rvdw = rcoulomb, so I used the -scalevdw option (which sh
