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
>
>
>
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>
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Received on Thu Oct 20 2016 - 10:30:02 PDT
