Thank you very much for the reply. It is actually working now.
On Fri, Aug 16, 2019 at 10:41 PM David Cerutti <dscerutti.gmail.com> wrote:
> What do you mean by 'distorted?' Is the ratio of box lengths changing? If
> so, then make sure to set the barostat to do isotropic rescaling, ntp = 1,
> not ntp = 2 or 3. If the system appears to be moving out of the water box,
> this is just the periodic boundary conditions at work, and you can make the
> result look pretty by centering the wrapped box on the centroid of your
> system. If the water content of the box seems to be developing cavities or
> looking like a block of swiss cheese at the corners, then this is likely
> the result of not equilibrating the volume under ntp in the first
> place--the system is forming a vacuum bubble (one, not many even though it
> may look like many if the bubble occurs on an edge or corner of the box).
>
> Dave
>
>
> On Fri, Aug 16, 2019 at 12:18 AM Airy Sanjeev <airy.sanjeev01.gmail.com>
> wrote:
>
> > Hello Amber User,
> > I am doing potential of mean force calculation for dimer structure using
> > umbrella sampling method. While running the production run, the waterbox
> is
> > getting distorted. I have used iwrap command but even then the waterbox
> is
> > not properly oriented. Kindly help in this regard.
> >
> > Thanking you in advance
> >
> >
> > --
> > with best regards,
> >
> > *Airy Sanjeev, PhDPost Doctoral Fellow*
> > *Indian Institute of Technology Guwahati, Guwahati*
> > *Assam-781039, India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
with best regards,
*Airy Sanjeev, PhDPost Doctoral Fellow*
*Indian Institute of Technology Guwahati, Guwahati*
*Assam-781039, India*
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Received on Mon Aug 19 2019 - 00:00:02 PDT
