Hi,
The binary file helps to improve the bond length consistency.
Thank you so much,
Zhiye
On Thu, Oct 10, 2013 at 12:23 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Oct 10, 2013 at 2:54 PM, Zhiye Tang <ztang006.ucr.edu> wrote:
>
> > Hi,
> >
> > I ran a MD simulation with pmemd.cuda for a pure water box of 1994 water
> > molecules with SHAKE algorithm turned on. But when I checked the bond
> > length and H-O-H angle of the water molecules, they still fluctuated for
> > around 0.1~0.2. In my case I need to make the water molecule perfectly
> > rigid.
> >
> >
>
>
> > The input file of a test run is given below,
> >
> > $cntrl
> > imin=0, irest=1, ntx=5,
> > ioutfm=0,
> >
>
> I think this is your problem. Set ioutfm=1 to print a NetCDF file instead
> of ASCII trajectory file. In your simulation, I believe that the bonds ARE
> being constrained to the same values (the SETTLE algorithm is analytical),
> but your trajectory is printed out in a precision with only 3 decimal
> places! Using NetCDF trajectories will store numbers to higher precision
> and give you a more accurate measure of bond lengths.
>
> So I don't think the error is in the bond lengths, but rather in how you
> are measuring them.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Oct 10 2013 - 14:00:04 PDT
