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 - 12:30:05 PDT
