Also... I'm pretty sure they shouldn't be negative. So, I might need
a lot of details.
If you already figured it out, just let us know.
On Mon, Apr 8, 2019 at 11:24 AM Lachele Foley <lf.list.gmail.com> wrote:
>
> Sorry to take so long to respond. There's lots going on.
>
> Can you tell me more molecular details about your system?
> Specifically, how large is the 'proteo' part and how large is the
> 'glycan' part? Feel free to send the input prmtop and inpcrd to me
> (to just me is fine). Thanks!
>
> On Tue, Apr 2, 2019 at 7:05 AM Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
> >
> > Dear AMBER user and developers,
> > I am trying to simulate a proteoglycan structure using conventional
> > molecular dynamics technique. Everything seems to be fine in the output
> > file where only the dihedral energy is showing a negative value. So why am
> > I getting the negative value in dihedral energy? Is there any discrepancy
> > in my system?
> > Secondly, when I am trying to simulate the same system using amd or gamd in
> > dual boost mode, but dihedral boost potential remains zero throughout our
> > simulation. As discussed in the gamd archive it is because of the negative
> > dihedral energy.
> > So is it an error to get negative dihedral energy or can I use the single
> > potential boost in amd or gamd technique?
> > It will be beneficial for me if you clarify all these doubts.
> > Thank you in advance!
> >
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 08 2019 - 09:00:02 PDT
