Thank you for your reply, Dave. It did not go to the list, but I am
replying to the list, so that the record is complete.
We will try assigning a real atomic number to the dummy particles. Does the
mass have any effect on the MD if the particles have no charge and are
given their own Lennard-Jones types?
I do not think we had “go” at the end of the Parmed script. We will use
that going forward.
We appreciate your help.
Sally
On Tue, Oct 4, 2022 at 12:40 PM David A Case <david.case.rutgers.edu> wrote:
> On Mon, Oct 03, 2022, Sally Pias wrote:
> >
> >I am working with Qi on this project and will attempt to explain what we
> >are trying to do. We are placing dummy atoms at specific points around a
> >curved lipid bilayer, to serve as a "wall" or physical guide to keep the
> >curvature in place. The curvature is to be maintained through
> Lennard-Jones
> >repulsion between the dummy atoms and the carbon atoms of the lipid
> >molecules.
> >
> >We originally defined new atom types, AN and SH, to serve as dummy
> >particles. (The AN particles were to be immobile and noninteracting, while
> >the SH particles were to be slightly mobile and LJ repulsive.) We gave
> them
> >an atomic number of -1, which seems to have signaled to Amber (pmemd.cuda)
> >that we were using "extra points" (EP).
>
> I'd have to study the code to know for sure what is happening, but the
> easiest thing to try is to give these atoms some real atomic number, so
> that
> they also get a mass (needed for any MD). You could use 10 or 18 (for Ne
> or
> Ar) as a start.
>
> >If needed, Qi can provide the specific series of commands used to generate
> >the prmtop file with Parmed. In short, we used the outparm command. When
> we
> >tried parmout, instead, Parmed did not generate a prmtop but gave no
> error.
>
> Did you have "go" command at the end of the parmed script? The file
> specified in a "parmout" statement is only written when "go" is executed.
> This makes it different from "outparm". See the on-line help for these
> three commands.
>
> ....good luck....dac
>
> --
Sally Pias
sallypias.gmail.com
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Received on Wed Oct 05 2022 - 16:30:03 PDT
