On Thu, Sep 29, 2016 at 9:01 AM, Debodyuti Dutta
<dutta.debodyuti.gmail.com> wrote:
> Dear Amber users,
> During the NPT equilibration, the volume of the system initially decreases
> for few steps. After that it become constant. What can be the possible
> reason for that (please give some references)?
If your system's density was too low (as is the case when you e.g.
build a solvated system using TIP3PBOX) the volume (i.e. the size of
the periodic cell) will decrease to compensate. Once the system
density starts to reach equilibrium the box size will level off. In
fact, a more or less stable density value is a good check that your
solvated system is reaching equilibrium.
-Dan
> The system after NVT heating was used for the starting point of NPT
> equilibration. I read only the coordinates, not the velocity.
>
> *Debodyuti Dutta*
> Research Scholar
> Indian Institute of Technology Kharagpur
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Sep 29 2016 - 06:30:04 PDT
