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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Received on Thu Oct 20 2016 - 08:30:02 PDT
