points like in TIP4P need to have their positions defined based on other
atoms - take a look at the existing code for details and to see how you
might adapt this to your system. I believe that most people give their
dummy atoms masses.
On Oct 20, 2016 1:03 PM, "Samuel Walpole (PHA)" <S.Walpole.uea.ac.uk> wrote:
> Thank you for your reply. I've read that this can be achieved by
> considering the dummy atom as an 'extra point', such as the extra point in
> TIP4P water. How would I define my dummy atom as an extra point in leap?
> The documentation doesn't seem to go into this.
>
> Best wishes,
> Sam
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: 20 October 2016 16:03
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Adding a Dummy Atom to Benzene
>
> if you plan to have this atom be propagated in time, then it needs to have
> a mass. you can only have a massless particle if the code defines it's
> position based on positions of atoms that are integrated using F=ma.
>
> On Thu, Oct 20, 2016 at 10:59 AM, Samuel Walpole (PHA) <
> S.Walpole.uea.ac.uk>
> wrote:
>
> > Dear Amber users,
> >
> > I am currently trying to set up a system containing benzene with a
> > massless dummy atom at its geometric centre. So far I have tried
> > creating a
> > mol2 file containing benzene and the dummy atom, with the dummy atom
> > type defined as DU. In the mol2 the dummy atom is bound to each of the
> > 6 carbon atoms, such that it has 6 single bonds in total. I have then
> > built the system in leap using a frcmod file generated by prmchk.
> > However, when I try to run a simulation, the benzene molecules become
> > very distorted and the temperature of the system heats to ~30,000 K (I
> am trying to run at 300 K).
> > I suppose that the problem is my parameters for my dummy atom are wrong.
> > Below is the frcmod that I am currently using:
> >
> > MASS
> > DU 0.000 0.000
> >
> > BOND
> > ca-DU 500.00 1.400
> >
> > ANGLE
> > ca-ca-DU 0.000 0.000
> > ca-DU-ca 0.000 0.000
> > ha-ca-DU 0.000 0.000
> >
> > DIHE
> > ca-ca-DU-ca 1 0.000 0.000 0.000
> > ca-DU-ca-ha 1 0.000 0.000 0.000
> >
> > IMPROPER
> > ca-ca-ca-ha 1.1 180.0 2.0
> > ca-ca-ca-DU 0.000 0.000 0.000
> >
> > NONBON
> > DU 0.0000 0.0000 0.000
> >
> > I suppose that I need non-zero parameters for the angle and dihedrals
> > to the dummy atom, but I have no idea what would be reasonable. Does
> > anyone who has any experience with dummy atoms have any suggestions as
> > to how I might solve this problem?
> >
> > Many thanks,
> > Sam Walpole, PhD Student
> > CAP 01.06
> > School of Pharmacy
> > University of East Anglia
> > Norwich Research Park
> > NR4 7TJ
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 21 2016 - 05:30:03 PDT
