Dear Jason,
Thank you for reply. I have added the non-bonded dummy atoms to the
topology file and do some SMD simulations vi sander without any problems.
Nevertheless, the problem is with pmemd. Does the way you suggested for
adding the dummy atom enable pmemd to support simulations with the dummy
atoms?
Best regards,
AMNN
On Thu, Aug 30, 2012 at 11:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Aug 30, 2012 at 2:29 PM, Ali M. Naserian-Nik
> <naseriannik.gmail.com>wrote:
>
> > I have tried to perform SMD simulations with the aid of the dummy atoms
> > using pmemd but, as you said too, normally pmemd calculations does not
> > support the dummy atom and the simulation did not proceed with error. I
> am
> > searching a way that enables me to use the dummy atom within pmemd
> > simulations.
>
>
> Why can't you just add the dummy atoms to the topology file? You could
> actually do this with ParmEd. Add some ions where you want your dummy
> atoms, then use xparmed.py to remove the charge, the van der waals terms,
> and create whatever bonds you want between the system and the dummy atom
> with whatever force constant you want. You can also change the mass and
> atom name/type, as well. The GUI xparmed.py interface as well as the
> manual should provide all the help you need to get started.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu Aug 30 2012 - 12:30:02 PDT
