if you search the archives for "iwrap" or "image" you will find lots of
information about this. ptraj can image your trajectory- there is probably
nothing wrong.
On Thu, Feb 12, 2009 at 4:48 PM, iccy liu <hbliu92.hotmail.com> wrote:
>
> Hi,
>
> Thanks a lot for your kind help in advance.
>
> I met a very strange situation. I set up a NVT calculation with periodic
> bounary condition using the input script below. However when I checked the
> trajectory and restart file, I found out the box size is the same as in my
> inpcrd file, however there are several molecules (more than 20) are out of
> the box. Some of them are 20A away from the bounary. I couldn't figure out
> why. My understanding is that if a molecule move out of the box, the peridic
> boundrary conditions will place it back in the other side of the box. Did
> anyone has similar problem before? Or just my input file has problems and
> the simulation wasn't go as the way I thought? Any input will be highly
> appreciated.
>
>
> input scirpt
> ---------------------------
>
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=5000, dt=0.0005,
> ntc=2, ntf=2,
> ntt=1,
> tempi=0.0, temp0=50.0,
> ntpr=100, ntwx=500, ntwx=1000,
> ntb=1, igb=0,
> cut=12.
> /
> ----------------------
>
>
> Sincerely,
>
> Iccy
>
> _________________________________________________________________
> More than messages–check out the rest of the Windows Live™.
>
> http://www.microsoft.com/windows/windowslive/_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 13 2009 - 01:21:41 PST
