Hello Prof. Ross Walker,
Thank you for sharing your thoughts.
As you correctly pointed out, many people have first equilibrated the
system in NPT to achieve stable density and then the switched to NVT for
production run.
I will reply in this email chain if I get any new insights from the authors
of the paper.
Regards,
Harsh
On Fri, Aug 19, 2016 at 7:43 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Harsh,
>
> I am not sure it is a specific requirement but I could certainly perceive
> that there might be issues with running it in NPT if the virial is not
> properly defined. That said one could use the Monte Carlo barostat which
> does not need a virial and I don't see any reason why that would not work.
> Ultimately though it might be better to equilibrate well in NPT and then
> switch on scaled MD in NVT. You may want to contact the authors of the
> paper (I don't think they are subscribed to this list) and ask them
> directly. If you get a definitive answer please post it back here so myself
> and others can read it.
>
> All the best
> Ross
>
> > On Aug 19, 2016, at 02:20, Harshavardhan Khare <harshkhare.gmail.com>
> wrote:
> >
> > Hi,
> >
> > I am wondering if scaled MD (in Amber 14) is required to be performed in
> > NVT ensemble.
> > I have come across a few papers, all of which have mentioned NVT for
> > production scaled MD. On the other hand, the conventional (or standard)
> MD
> > and even the accelerated MD simulations seem to be frequently performed
> in
> > NPT ensemble.
> > Is there any specific reason for not using NPT for scaeld MD?
> >
> > regards,
> > Harsh
> > -------------
> > Harshavardhan Khare,
> > Dept. of Physics,
> > Indian Institute of Science,
> > Bangalore
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>
>
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Received on Fri Aug 19 2016 - 22:30:02 PDT
