Send it to my personal email (lf.list.gmail.com).
On Tue, Apr 9, 2019 at 3:56 AM Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
>
> Dear Mam,
> Did you receive the topology file? In amber mailing list is not allowing me
> to send those files because of the size issue.
>
> On Tue, Apr 9, 2019 at 9:13 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
>
> > Dear Mam,
> > I am not still able to figure it out. I am simulating a proteoglycan chain
> > only. So there is no protein part. My chain just consists of dermatan
> > sulphate only. Please check my topology and coordinate files. I am not able
> > to find any error or discrepancy in output files or by visualization.
> > Thank you in advance
> >
> > On Mon, Apr 8, 2019 at 9:20 PM Lachele Foley <lf.list.gmail.com> wrote:
> >
> >> 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
> >>
> >
> >
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> >
>
>
> --
> *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
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Received on Tue Apr 09 2019 - 11:00:02 PDT
